Targeted hd5 antibody and assay methods for diagnosing and treating inflammatory bowel disease

ABSTRACT

A targeted DEFA5 antibody is disclosed herein. The targeted DEFA5 antibody has a high degree of specificity with DEFA5 protein, particularly with peptide sequences of the P, B, and/or M binding sites of the DEFA5 protein. The targeted DEFA5 antibody may be incorporated into an assay for diagnosing and treating ulcerative colitis and Crohns disease in a subject suffering from inflammatory bowel disease. The assay may be provided in a kit. The targeted DEFA5 antibody may be used in a method for measuring the level of DEFA5 or DEFA5 expression in a sample collected from a subject, and determining, based on the level of DEFA5 or DEFA5 expression, whether the subject is suffering from ulcerative colitis or Crohns disease. A treatment may be based on the determination of whether the subject has ulcerative colitis or Crohns disease.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application cites and claims priority of U.S. Patent Application No. 62/522,652, filed Jun. 20, 2017 (currently pending).

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under grant numbers R21DK095186; U54CA091408-09S1; U54CA091408-09S2; U54RR026140; U54MD007593; UL1RR024975; UL1TR000445; G12MD007586; U54CA163069; R24 DA036420; and S10RR0254970 awarded by the National Institute of Health. The government has certain rights in the invention.

In this context “government” refers to the government of the United States of America.

BACKGROUND OF THE DISCLOSURE

Inflammatory bowel disease (IBD) is the chronic inflammation of all, or part of, the digestive tract. Common causes of IBD include ulcerative colitis (“UC”) and Crohn's disease, also known as Crohn's colitis (“CD” or “CC”). Ulcerative colitis causes chronic inflammation and ulcers in the innermost lining of the large intestine, i.e. the colon, and rectum. Crohn's disease causes chronic inflammation of the lining of the digestive tract, where inflammation goes beyond the lining and into affected tissue. Crohn's disease can affect the small intestine, large intestine, or both.

UC and CD affect an estimated 1.6 million people in the US alone with associated annual health care costs of over $6.3 billion. While UC and CD are both types of IBDs, differences between patients having UC or CD have major implications. Currently, clinicians use inexact combined classifications for patients having IBD, which include clinical, endoscopy, radiological, and histopathology in an effort to diagnose CD and UC. Nonetheless, differentiating patients having UC or CD among patients suffering from IBD remains challenging, so much so that cases of patients having IBD that are difficult to classify as UC or CD are classified as having indeterminate colitis (“IC”). A significant subgroup of IBD patients are misdiagnosed or have a correct diagnosis delayed despite use of a state-of-the-art classification system applying clinical, endoscopic, radiologic, and histologic tools. Indeed, it is estimated that 30% of patients suffering from IBD cannot currently be accurately diagnosed as CD or UC.

In addition, 15% of colonic IDB cases that undergo ileal pouch anal anastomosis surgery, as they are diagnosed with UC, will subsequently have their original diagnosis changed to CD based on their postoperative follow-up visits, clinical and histopathology changes, and development of de novo CD in the ileal pouch. Ileal pouch anal anastomosis, a treatment normally suitable for UC but not CD, restores gastrointestinal continuity after surgical removal of the colon and rectum, and involves the creation of a pouch of small intestine to recreate the removed rectum.

Implications of distinguishing cases of UC and CD include choice of medical treatment, timing of surgery, prognosis, whether to offer the patient an ileal pouch anal anastomosis, and lifestyle expectations. For these reasons, there is a need for improving the diagnosis, and subsequent treatment, of subjects having IBD.

SUMMARY

It has been discovered that the DEFA5 protein (e.g., HD5), and the expression of the DEFA5 gene, may serve as a biomarker for determining whether a patient suffering from IBD has UC or CD. In particular, an anti-DEFA5 antibody has been identified and discovered that has high specificity for binding with DEFA5 while not binding with other defensin proteins that is highly advantageous for identifying DEFA5 as a biomarker in subjects.

In a first aspect, a method of measuring DEFA5 protein in a patient suffering from or at risk of inflammatory bowel disease (IBD) is disclosed. The method includes measuring the level of DEFA5 or DEFA5 expression in a sample from the subject using an anti-DEFA5 antibody.

In a second aspect, a method of treating a patient suffering from or at risk of IBD is disclosed. The method includes measuring the level of DEFA5 or DEFA5 expression in a sample from the subject using an anti-DEFA5 antibody and performing an intervention on the patient to treat Crohn's disease. The method may further comprise comparing the expression of DEFA5 or the concentration of DEFA5 in the sample to a benchmark value that is typical of a subject not suffering from Crohn's disease; and diagnosing Crohn's disease if the expression of DEFA5 or the concentration of DEFA5 in the sample significantly exceeds the benchmark value.

In a third aspect, a method diagnosing a subject suffering from or at risk of CD is provided, comprising measuring the level of DEFA5 or DEFA5 expression in a sample from the subject using an anti-DEFA5 antibody; comparing the expression of DEFA5 or the concentration of DEFA5 in the sample to a benchmark value that is typical of a subject not suffering from Crohn's disease; and diagnosing Crohn's disease if the expression of DEFA5 or the concentration of DEFA5 in the sample significantly exceeds the benchmark value.

In a fourth aspect, a method for treating a patient suffering from or at risk of UC is disclosed. The method comprises performing the method of measuring DEFA5 in the patient according to the first aspect; and performing an intervention on the patient to treat ulcerative colitis. The method may further comprise comparing the expression of DEFA5 or the concentration of DEFA5 in the sample to a benchmark value that is typical of a subject not suffering from Crohn's disease; and diagnosing ulcerative colitis if the expression of DEFA5 or the concentration of DEFA5 in the sample does not significantly exceed the benchmark value.

In a fifth aspect, a kit for measuring DEFA5 in a sample is provided. The kit comprises an assay comprising an anti-DEFA5 antibody; and a sample container configured to contain a sample selected from: a stool sample, a blood sample, a bowel tissue sample, and a serum sample. The kit may be for the diagnosis, and subsequent treatment of, inflammatory bowel disease. The kit comprises any of the anti-DEFA5 antibodies disclosed herein as part of immunoassay. The antibodies may be tagged, conjugated, truncated, or otherwise modified to function in the assay as is known in the art. The kit may further comprise one or more of a sample container and a sampling tool. The container and sampling tool may be configured to collect and store various types of samples including a stool sample, a blood sample, a serum sample, a rectal lavage sample, and a biopsy sample. The sampling tool may be any of a biopsy instrument, a rectal lavage kit, a swab, a blood sampler, and a vacutainer.

In a sixth aspect, a method of diagnosing and treating Crohn's disease in a subject suffering from inflammatory bowel disease is provided. The method includes obtaining a sample from the patient; measuring the concentration of human DEFA5 in the sample using an anti-DEFA5 antibody having a higher affinity for human DEFA5 than for either of human DEFA1 or human DEFA6; comparing the concentration of DEFA5 in the sample to a benchmark value that is typical of a subject not suffering from Crohn's disease; diagnosing Crohn's disease if the concentration of DEFA5 in the sample significantly exceeds the benchmark value; and treating the subject for Crohn's disease by way of a non-surgical intervention.

The above presents a simplified summary in order to provide a basic understanding of some aspects of the claimed subject matter. This summary is not an extensive overview. It is not intended to identify key or critical elements or to delineate the scope of the claimed subject matter. Its sole purpose is to present concepts in a simplified form as a prelude to the more detailed description that is presented later.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a dot staining of HD1 to HD6 specificity of commercially available DEFA5 antibodies.

FIG. 2A illustrates an alignment of the primary sequence of DEFA5 with that of HD1 and HD6.

FIG. 2B is a schematic showing DEFA5 antibody epitopes to distinguish pro-DEFA5 from mature protein in sera of IBD patients.

FIG. 2C is a model of sandwich ELISA to be used to detect pro-DEFA5 and mature DEFA5 in sera of IBD patients.

FIG. 3A shows initial diagnostic information of 21 subjects diagnosed with ulcerative colitis, indeterminate colitis, or Crohn's disease.

FIG. 3B shows diagnostic information of the 21 subjects reevaluated 9.4 years after the initial diagnostic information of FIG. 3A.

FIGS. 4A-4C are histological staining of DEFA5 tissue samples from patients treated with various treatments.

FIG. 4D is a quantification of staining spot counts for ulcerative colitis RPC and IPAA-operated patients who did not have their original diagnosis changed versus those who did change from ulcerative colitis to de novo Crohn's disease.

FIGS. 5A-5I illustrate histological staining on parallel sections for the typical morphological appearance of Paneth cell (PCs) including the presence of dense apical eosinophilic granules.

FIGS. 6A-6J illustrate a double histological stain of PCs, lysosomes, and DEFA5.

FIG. 7A illustrates quantification of DEFA5 transcript levels in moderate UC and CC samples.

FIG. 7B illustrates a DEFA5 western blot showing higher DEFA5 levels in moderate and severe CC compared to other IBD disease states.

FIG. 7C illustrates DEFA5 levels in various IBD disease states.

FIGS. 7D-7H illustrate IHC staining of DEFA5 in colonic tissues using formalin-fixed paraffin-embedded thin sections.

FIGS. 8A-8F illustrate representative H&E staining of colonic resected tissues.

FIGS. 9A-9D illustrate IHC and H&E staining of DEFA5 in adjacent normal and diseased tissues from CC patients (A and B) and from UC patients (C and D).

FIGS. 10A-10C illustrate detection of DEFA5 in IBD patient sera and specificity of available DEFA5 antibodies.

FIGS. 11A and 11B illustrate the distribution of collected fresh frozen tissue and blood samples from IBD and non-IBD patients by sex and race.

DETAILED DESCRIPTION

Unless otherwise defined, all terms (including technical and scientific terms) used herein have the same meaning as commonly understood by one of ordinary skill in the art of this disclosure. It will be further understood that terms, such as those defined in commonly used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the specification and should not be interpreted in an idealized or overly formal sense, unless expressly so defined herein. Well-known functions or constructions may not be described in detail for brevity or clarity.

The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting. As used herein, the singular forms “a”, “an,” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise.

The term “consisting essentially of” means that, in addition to the recited elements, what is claimed may also contain other elements (steps, structures, ingredients, components, etc.) that do not adversely affect the operability of what is claimed for its intended purpose as stated in this disclosure. This term excludes such other elements that adversely affect the operability of what is claimed for its intended purpose as stated in this disclosure, even if such other elements might enhance the operability of what is claimed for some other purpose.

The terms “about” and “approximately” shall generally mean an acceptable degree of error or variation for the quantity measured given the nature or precision of the measurements. Typical, exemplary degrees of error or variation are within 20%, preferably within 10%, and more preferably within 5% of a given value or range of values. For biological systems, the term “about” refers to an acceptable standard deviation of error, preferably not more than 2-fold of a given value. Numerical quantities in this detailed description are approximate unless stated otherwise, meaning that the term “about” or “approximately” can be inferred when not expressly stated.

The terms “individual,” “subject,” or “patient” as used herein refer to any animal, including mammals, such as mice, rats, other rodents, rabbits, dogs, cats, swine, cattle, sheep, horses, primates, and humans. The terms may specify male or female or both, or exclude male or female.

The terms “treatment”, “treat”, and “treating”, as used herein, refer to a course of action (such as administering a compound or pharmaceutical composition) initiated after the onset of a clinical manifestation of a disease state or condition so as to eliminate or reduce such clinical manifestation of the disease state or condition.

Such treating need not be absolute to be useful.

The terms “first”, “second”, and the like are used herein to describe various features or elements, but these features or elements should not be limited by these terms. These terms are only used to distinguish one feature or element from another feature or element. Thus, a first feature or element discussed below could be termed a second feature or element, and similarly, a second feature or element discussed below could be termed a first feature or element without departing from the teachings of the present disclosure.

DEFA5 is a small, microbicidal innate immune system protein belonging to the alpha defensin family of mammalian defensin peptides. DEFA5 is expressed in various tissues and particularly on mucosal surfaces. DEFA5 is encoded by the gene DEFA5. DEFA5 is involved in host defense mechanisms and is highly expressed in secretory granules of Paneth cells of the small intestine (ileum). Like most secreted proteins, DEFA5 is synthesized as prepro-DEFA5 (1-94) that undergoes proteolytic processing first, to the inactive pro-DEFA5s (20-94), DEFA5 (23-94), and DEFA5 (29-94). DEFA5 (23-94) and DEFA5 (29-94) are found within tissues, while DEFA5 (20-94) is the predominant intracellular form. The pro-DEFA5s are then processed to two active or mature forms. DEFA5 (56-94) and DEFA5 (63-94) with DEFA5 (63-94) being the most abundant form. These mature forms of DEFA5 are cysteine-rich host defense peptides which exert broad-spectrum antimicrobial activity and contribute to innate immunity in the human gut. As used herein, DEFA5 may refer to exclusively mature forms of DEFA5.

Methods of using an anti-DEFA5 antibody are described herein, whereby the anti-DEFA5 antibody is used in the detection, measurement, and/or treatment of patients having IBD. The anti-DEFA5 antibody forms a complex with DEFA5 that is relatively stable under physiologic conditions. Specific binding can be characterized by an equilibrium dissociation constant of at least about 1×10⁻⁶ M or less (e.g., a smaller KD denotes a tighter binding). Methods for determining whether two molecules specifically bind are well known in the art and include, for example, equilibrium dialysis, surface plasmon resonance, and the like. An anti-DEFA5 antibody may, however, exhibit cross-reactivity to other antigens such as DEFA5 molecules from other species. Moreover, multi-specific antibodies (e.g., bispecifics) that bind to DEFA5 and one or more additional antigens are nonetheless considered anti-DEFA5 antibodies, as used herein. As used herein, an “anti-DEFA5 antibody” is an antibody that forms a stable complex with DEFA5 under expected binding conditions (e.g., physiological conditions).

The anti-DEFA5 antibody may bind to DEFA5 at various levels of affinity. One embodiment of the anti-DEFA5 antibody is a high affinity anti-DEFA5 antibody. The term “high affinity” antibody refers to an antibody having a binding affinity to DEFA5 of at least 10⁻¹⁰ M; preferably 10⁻¹¹ M; even more preferably 10⁻¹² M, as measured by surface plasmon resonance, e.g., BIACORE™ or solution-affinity ELISA.

The anti-DEFA5 antibody may bind to DEFA5 with high affinity (“high-affinity anti-DEFA5 antibody”). As used herein, a “high affinity anti-DEFA5 antibody” is an antibody that has a high binding affinity. “High binding affinity” refers to a high strength with which the epitope binds to an individual paratope (antigen-binding cite). Antibodies that have a high binding affinity bind more quickly to the antigen, permit greater sensitivity in assays, and better maintain a bond with the paratope when compared to an antibody having a lower affinity. The anti-DEFA5 antibody described herein may have a binding affinity to DEFA5 of at least as low as 10⁻⁷, 10⁻⁸, 10⁻⁹, 10⁻¹⁰, 10⁻¹¹, or 10⁻¹² KDs (M), or any range or subvalue thereof, The term “KD” refers to the equilibrium dissociation constant of a particular antibody-antigen interaction, or the equilibrium dissociation constant of an antibody, antibody binding fragment, or molecular interaction. The equilibrium dissociation may be calculated by obtaining the dissociation rate constant (koff value) of a particular antibody-antigen interaction, with the association rate constant of a particular antibody-antigen interaction. A lower KD value indicates a higher binding affinity.

The anti-DEFA5 antibody described herein may also have a high specificity to DEFA5. A “specificity” refers to the ability to bind to a particular antigen, but not other antigens. Some embodiments of the anti-DEFA5 antibody display an affinity for DEFA5 that exceeds a displayed affinity to one or more related proteins; such related proteins may include one or more of DEFA1, DEFA2, DEFA3, DEFA4, and DEFA6. These are related neutrophil defensins found in multiple species. The canonical human neutrophil defensin 1 protein (DEFA1) is described at UniProt Accession No. P59665, the sequence of which is provided herein as SEQ ID NO: 2. The canonical human neutrophil defensin 2 protein (DEFA2) is described at UniProt Accession No. P59665, the sequence of which is provided herein as SEQ ID NO: 3. The canonical human neutrophil defensin 3 protein (DEFA3) is described at UniProt Accession No. P59666, the sequence of which is provided herein as SEQ ID NO: 4. The canonical human neutrophil defensin 4 protein (DEFA4) is described at UniProt Accession No. P12838, the sequence of which is provided herein as SEQ ID NO: 5. The canonical human neutrophil defensin 6 protein (DEFA6) is described at UniProt Accession No. P12838, the sequence of which is provided herein as SEQ ID NO: 6. Further embodiments of the high specificity anti-DEFA5 antibody display a higher affinity to DEFA5 than to DEFA1, DEFA6, or both. In an embodiment, the anti-DEFA5 antibody has a high specificity to DEFA5 and does not bind, or substantially does not bind (i.e., has a low or no binding affinity), to HD1 and HD6. The anti-DEFA5 antibody may have a binding affinity to HD1 and/or HD6 of greater than about 10⁻¹⁰, 10⁻⁹, 10⁻⁸, 10⁻⁷, 10⁻⁶, 10⁻⁵, 10⁻⁴, 10⁻³, 10⁻², 10⁻¹ Kos (M), or any range or subvalue thereof. The anti-DEFA5 antibody may have a KDs (M) with one or both of DEFA1 and DEFA6 that is greater than one of the following values: 10⁻¹⁰, 10⁻⁹, 10⁻⁸, 10⁻⁷, 10⁻⁶, 10⁻⁵, 10⁻⁴, 10⁻³, 10⁻², and 10⁻¹. The anti-DEFA5 antibody may recognize an epitope binding region having at least 80%, 85%, 90%, 92%, 94%, 96%, or 98% sequence identity to positions 51-94 of SEQ ID NO: 1. The anti-DEFA5 antibody may recognize an epitope binding region having 100% sequence identity to positions 51-94 of SEQ ID NO: 1. Some embodiments of the anti-DEFA5 antibody do not recognize an epitope binding region having at least 80%, 85%, 90%, 92%, 94%, 96%, or 98% sequence identity to positions 1-49 of SEQ ID NO: 1. A specific embodiment of the anti-DEFA5 antibody does not recognize an epitope binding region having 100% sequence identity to positions 1-49 of SEQ ID NO: 1.

Examples of commercially available anti-DEFA5 antibodies include: Anti-alpha 5 Defensin antibody [EPR14309(B)] from ABCAM, Cambridge, United Kingdom; Anti-alpha 5 Defensin antibody (ab167591) from ABCAM, Cambridge, United Kingdom; Anti-alpha 5 Defensin antibody [8C8] (Catalogue #ab90802) from ABCAM, Cambridge, United Kingdom; Defensin 5 Monoclonal Antibody (8C8) (Catalogue #MA1-46026) from THERMO FISHER SCIENTIFIC INC., Waltham, Mass.; Anti-Alpha Defensin-5 (DEFA5) Antibody, clone 8C8 (Catalogue #MABF31) from MILLIPORESIGMA, Burlington, Mass.; Defensin 5 Antibody LS-C50934 (Catalogue #LS-C50934-100) from LSBIO, Seattle, Wash.; Defensin alpha 5 Antibody (8C8) (Catalogue #NB110-60002/NB110-60002SS) from NOVUS BIOLOGICALS, Littleton, Colo.; Defensin alpha 5 Antibody (8C8) (Catalogue #NBP1-84282) from NOVUS BIOLOGICALS, Littleton, Colo.; Defensin alpha 5 antibody (Catalogue #orb156565) from BIORBYT, Cambridge, United Kingdom; Defensin alpha 5 Antibody (Catalogue #bs-4313R) from BIOSS INC., Woburn, Mass.; Defensin alpha 5 antibody [N1C3] (Catalogue #GTX116079) from GENETEX, INC., Irvine, Calif.; Anti-DEFA5 Antibody (HPA015775) from ATLAS ANTIBODIES, Bromma, Sweden; DEFA5 antibody (catalogue number 972207.111 or CSL 1450400) from R&D SYSTEMS, Minneapolis, Minn.; and α-defensin 5 antibody (catalogue #53997) from SANTA CRUZ BIOTECHNOLOGY, INC., Dallas, Tex., among many others.

In one embodiment, the anti-DEFA5 antibody is α-defensin 5 antibody (catalogue #53997) from SANTA CRUZ BIOTECHNOLOGY, INC., Dallas, Tex. Surprisingly, it has been discovered that the α-defensin 5 antibody (catalogue #53997) is particularly advantageous for measuring the levels of DEFA5 and DEFA5 expression in a sample. In particular, the α-defensin 5 antibody (catalogue #53997) displays a high affinity and high specificity for DEFA5, including the high affinity and high specificity for HD5 and low to no affinity and specificity for other defensins, such as HD1-HD4 or HD6. The anti-DEFA5 antibody may be a kappa light chain polypeptide subunit. In some embodiments, the anti-DEFA5 antibody is a mammalian antibody, such as a human antibody or a canine antibody.

A method of diagnosing ulcerative colitis or Crohn's disease in a subject is disclosed. The subject may have IBD. The method includes measuring the level of α-defensin 5 (“DEFA5”) or DEFA5 expression in a sample from the subject using a anti-DEFA5 antibody, and diagnosing the subject as suffering from Crohn's disease if the level or expression of DEFA5 is indicative of a subject having Crohn's disease; or diagnosing the subject as suffering from ulcerative colitis if the level or expression of DEFA5 is indicative of a subject having ulcerative colitis. The sample can be taken from any suitable source for measuring DEFA5 concentration, DEFA5 expression levels, such as tissue samples from the intestine, such as from the large intestine or rectum. In this disclosure the term “expression of DEFA5” should be interpreted to mean the expression of the DEFA5 gene; “levels of DEFA5” should be interpreted to mean the concentration of DEFA5 protein.

The sample may be taken from a subject who is suffering from or at risk of IBD. The subject may display one or more symptoms characteristic of IBD, such as severe diarrhea, abdominal pain, fatigue, and weight loss. In some embodiments of the method, the subject displays more than one of said symptoms. In further embodiments the subject displays two, three, or four of said symptoms.

It has been discovered that DEFA5 is differentially expressed in subjects having UC and CD. Used in this way, DEFA5 concentration and DEFA5 expression can be utilized and measured, using the targeted DEFA5 antibody, as a biomarker for distinguishing UC and CD in patients having IBD. As ileal pouch anal anastomosis is clinically much more successful in patients having UC than in patients suffering from CD, patients identified as having levels of DEFA5 indicative of UC, or not having CD, may be treated with ileal pouch anal anastomosis. Indeed, as DEFA5 is produced by Paneth cells only, one would not expect to find Paneth cells that secret DEFA5 in the colon. It has been discovered that Paneth cells (secreting DEFA5) are abundantly found in subjects having CC. On the other hand, patients identified as having levels of DEFA5 and DEFA5 expression indicative of CD may be treated with any suitable treatment for CD. In an embodiment, a diagnosing step, such as diagnosing a subject with UC or CD, is optional.

The anti-DEFA5 antibody may have a complementarity determining region (CDR) that is complementary to each of, or all of, the DEFA5 sequence of the P, B, and M binding sites of DEFA5, as shown in FIG. 2. As used herein, “complementary to” means that the CDR is capable of forming a stable complex with the target sequence (e.g., the P, B, or M binding sites) under expected binding conditions (e.g., physiological conditions).

In another embodiment, the antibody may be an antibody having a certain degree of identity to a polypeptide sequence complementary to the P, B, and M binding sites of DEFA5. For example, the antibody may be at least 75%, 80%, 85%, 90%, 95%, 99%, 99.5%, or 100% identical to a complementary polypeptide sequence to polypeptide sequence of the P, B, and M binding sites of DEFA5.

Some embodiments of the antibody disclosed herein more specifically target DEFA5 than they do other alpha defensins. FIG. 1 illustrates dot blotting of the specificity of commercially available DEFA5 antibodies to purified HD1-HD6 proteins versus a Ponceau S control. As used herein, the term “specificity” or similar terms, used in the context of an antibody with regard to its target, refers to the antibody specifically binding to the target antigen (as opposed to other antigens, such as HD1, HD2, HD3, HD4, and HD6). This higher DEFA5 specificity of the present antibody would allow, for example, easier and more accurate testing of DEFA5 levels or expression in samples from subjects.

It is believed that there may be a dysfunction in the activation pathway of DEFA5 in patients suffering from moderate and severe CD, and thus, an excess amount of inactive form DEFA5 is a potential mechanism for inflammation in patients suffering from CD. This excessive amount of inactive form DEFA5 may cause increased damage to the epithelial lining and potentially even a dysregulation in the levels and make-up of gut flora.

The methods may include a step of comparing the level of the DEFA5 to a benchmark value. The benchmark value may be a measure of central tendency based on levels observed in one or more populations of subjects that are established to be unafflicted by either UC or CD. For example, the benchmark value may be a mean level of the gene expression or protein concentration observed in samples from a population of subjects who are unafflicted by UC, unafflicted by CD, or both. The population may be defined by one or more of the patient's geography, age, ethnicity, sex, and medical history. The benchmark value may take into account a measure of variation combined with a measure of central tendency. For example, the benchmark value may be a mean level of the gene expression or protein concentration observed in a given tumor population, plus or minus a margin of error. The benchmark may be based on raw measurements (such as fragments of mRNA or cDNA per kb gene length per million reads) or normalized measurements (such as % of normal expression, or expression compared to a constitutively expressed or widely expressed gene with generally consistent expression, such as β-actin). An example of a suitable benchmark value is about 1 ng/mL DEFA5 or exactly 1 ng/mL DEFA5.

The benchmark may also be established by analysis of a control sample that is measured alongside the sample from the subject. Examples of suitable control samples are: a sample from a subject unafflicted with UC, a sample from a subject unafflicted with CD, a sample from a subject afflicted with UC (although unafflicted with CD), a sample from a subject afflicted with CD (although unafflicted with UC), a sample from a subject afflicted with diverticulitis (although unafflicted with either UC or CD), and a sample from a subject unafflicted from IBD. In some embodiments, the benchmark value level may be a normal level, such as described, infra.

In an embodiment, an assay method of differentially diagnosing UC and CD in a patient suffering from IBD includes measuring the level of DEFA5 or DEFA5 expression present in a sample obtained from the patient. The level of DEFA5 or MMP-7 concentration or expression in the tissue may be measured by any suitable peptide analysis. For example, the measuring step may include one or more of enzyme-linked immunosorbent assay (ELISA), cation-ion exchange, NMR analysis, genome-wide transcriptome analysis, and mass spectrometry. The method may include comparing the concentration or expression of DEFA5 in the sample to the benchmark, and making a diagnosis if the concentration or expression of DEFA5 in the sample is significantly less than or significantly greater than the benchmark value. For example, the method may comprise comparing the concentration or expression of DEFA5 in the sample to the benchmark, and making a diagnosis of CD if the concentration or expression of DEFA5 in the sample is significantly greater than the benchmark value. As another example, the method may comprise comparing the concentration or expression of DEFA5 in the sample to the benchmark, and making a diagnosis of UC if the concentration or expression of DEFA5 in the sample is not significantly greater than the benchmark value. The measurement of the expression of DEFA5 or the concentration of DEFA5 in the sample may be measured in the same ex vivo or in vitro.

The difference in expression or concentration may be considered significant based on any of a variety of known statistical tests for significance. These are generally based on a collection of measurements made from a sampled population, and are affected by both the population size and the sampling size. Such statistical tests are well known in the art and are not further elaborated upon in this disclosure; outside references can be relied upon to enable those skilled in the art to determine statistical significance, such as Rosener's Fundamentals of Biostatistics, 8^(th) ed. (2015), Cengage Learning, Boston, Mass.

In an embodiment, an assay method of differentially diagnosing UC and CD in a patient suffering from IBD includes measuring the level of DEFA5 or DEFA5 expression present in a sample obtained from the patient. The level of DEFA5 or DEFA5 expression in the tissue may be measured by an enzyme-linked immunosorbent assay (ELISA) that uses the targeted DEFA5 antibody disclosed herein. The method includes diagnosing the patient as having UC if DEFA5 or DEFA5 expression is at any level that is indicative of a patient not having CD, such as less than 5× normal levels of DEFA5, or from less than about 5×-30× normal levels of DEFA5 or DEFA5 expression. In an embodiment, the patient is diagnosed as having UC if DEFA5 expression is at a level of less than 3×10⁶ DEFA5 mRNA Transcript per 10 ng RNA. The diagnosing may diagnose the patient as having CD if the level of DEFA5 expression is at any level indicative of a patient having CD, such as from about 3×10⁶ to 1.2×10⁸ DEFA5 mRNA Transcript per 10 ng RNA. As used herein, a “normal level” of DEFA5 or DEFA5 expression means a level of DEFA5 or DEFA5 expression in the digestive tract tissue from a subject not having CD or UC, or a subject suffering from IBD and specifically UC. Normal DEFA5 expression may refer to from 1×10⁵ to 9×10⁵ DEFA5 mRNA Transcript per 10 ng RNA, or about 6×10⁵ DEFA5 mRNA Transcript per 10 ng RNA.

In one embodiment, the assay methods involve determining the status of a subject with respect to the activity and/or expression of DEFA5 or the activity and/or expression of a polypeptide regulated by DEFA5. In one embodiment, such methods comprise determining the level of expression or activity of DEFA5 or a polypeptide regulated by DEFA5 in a sample from the subject with the targeted DEFA5 antibody disclosed herein. The method may further comprise collecting the sample from the subject. As used herein, a biological sample which is subjected to testing is a sample derived from a subject and includes, but is not limited to, any biological material, such as a bodily fluid. Examples of bodily fluids include, but are not limited to, whole blood, serum, saliva, tissue infiltrate, pleural effusions, lung lavage fluid, bronchoalveolar lavage fluid, and the like. The biological fluid may be a cell culture medium or supernatant of cultured cells. For example, the sample can be intestinal tissue, stool, blood, or serum. In embodiment, the biological sample is collected from the colon of a subject.

Some embodiments of the method comprise measuring the concentration of DEFA5 by selectively staining or dying the sample from the subject and measuring the signal from the stain. The stain or dye may comprise the any anti-DEFA5 antibody disclosed herein. The stain or dye may also comprise a reporter, such a colorimetric group, a radionuclide, a stable isotope, a fluorophore, a chromophore, an enzyme, a magnetic particle, and a quantum dot. The concentration of DEFA5 can then be measured by observing the signal from the reporter, such as by microscopy, colorimetry, radiometry, fluoroscopy, magnetotaxis, or any combination of the foregoing. In a specific embodiment of the method, the concentration of DEFA5 is measured by immunostaining the sample with an immunostain that recognizes DEFA5 and counting the number of stained cells by microscopy. This approach has the advantage of relative simplicity, and only requires the types of equipment that are already present in typical clinical laboratories. A diagnosis can be made based on a threshold number of cells that stain positive, such as at least 10%, 20%, and 30%. If the number of DEFA5 stained cells is significantly above the threshold value, than a diagnosis of CD can be made; whereas if the number of DEFA5 stained cells is significantly below the threshold value, than a diagnosis of UC can be made.

Those subjects in which DEFA5 activity and/or expression differs (increased or decreased) from a control or benchmark value or the activity of a polypeptide regulated by DEFA5 differs as compared to a control or benchmark value are determined to be suffering from or at risk for disease states and conditions associated with or characterized by increased or decreased DEFA5 activity.

Assay techniques that can be used to determine levels of expression or activity in a sample are known. Such assay methods include, but are not limited to, radioimmunoassays, reverse transcriptase PCR (RT-PCR) assays, immunohistochemistry assays, in situ hybridization assays, competitive-binding assays, Western Blot analyses, ELISA assays and proteomic approaches, two-dimensional gel electrophoresis (2D electrophoresis) and non-gel based approaches such as mass spectrometry or protein interaction profiling. Assays also include, but are not limited to, competitive and non-competitive assay systems using techniques such as radioimmunoassays, enzyme immunoassays (EIA), enzyme linked immunosorbent assay (ELISA), sandwich immunoassays, precipitin reactions, gel diffusion reactions, immunodiffusion assays, agglutination assays, complement-fixation assays, immunoradiometric assays, fluorescent immunoassays, protein A immunoassays, and immunoelectrophoresis assays. For examples of immunoassay methods, see U.S. Pat. Nos. 4,845,026 and 5,006,459. Any of the anti-DEFA5 antibodies disclosed herein may be in the assay.

The anti-DEFA5 antibody can be incorporated into an ELISA assay for the diagnosing methods. In addition, a reporter antibody generally is prepared. The reporter antibody is attached to a detectable reagent such as a radioactive, fluorescent, or enzymatic reagent, for example horseradish peroxidase enzyme or alkaline phosphatase. In one embodiment of the ELISA, to carry out the ELISA, the anti-DEFA5 antibody is incubated on a solid support that binds the antibody. Any free protein binding sites on the dish are then covered by incubating with a non-specific protein. Next, the sample to be analyzed is incubated with the solid support, during which time the anti-DEFA5 antibody binds to DEFA5. Unbound sample is washed out with a buffer. A reporter antibody specifically directed to the antigen and linked to a detectable reagent is introduced resulting in binding of the reporter antibody to any antibody bound to the antigen. Unattached reporter antibody is then washed out. Reagents for detecting the presence of the reporter antibody are then added. The detectable reagent is then determined in order to determine the amount of antigen present. In an alternate embodiment, the antigen is incubated with the solid support, followed by incubation with one or more antibodies, wherein at least one of the antibodies comprises a detectable reagent. Quantitative results may be obtained by reference to a standard curve.

A method of treating IBD in a patient suffering from IBD may include: (a) measuring the level of DEFA5 or DEFA5 expression present in a sample obtained from the patient with the anti-DEFA5 antibody, whereby a level of DEFA5 or DEFA5 expression is obtained; (b) if the level of DEFA5 or DEFA5 expression is at a level indicative of a patient not having CD, treating the IBD in the patient with a suitable medical treatment for UC; if the level of DEFA5 or DEFA5 expression is at a level indicative of a patient having CD, treating the IBD in the patient with a suitable medical treatment for CD.

Suitable medical treatments for UC include ileal pouch anal anastomosis or the administration of pharmaceutical agents or salts thereof. Suitable pharmaceutical agents may be one or more of: an iron supplement; an oral 5-aminosalicylate, such as mesalamine, balsalazide and olsalazine; an anti-inflammatory; a corticosteroid; an immunosuppressant such as azathioprine, mercaptopurine, methotrexate, and cyclosporine; an anti-TNF-alpha antibody such as infliximab, adalimumab, and golimumab; an anti-α4-integrin antibody such as vedolizumab; and an antibacterial antibiotic, such as ciprofloxacin and metronidazole. Surgeries that are sometimes used to treat UC include a total proctocolectomy, and an ileal pouch anal anastomosis. Note that ileal pouch anal anastomosis are recognized as relatively ineffective when used to treat CD, in contrast to UC. It should also be noted that cyclosporine and golimumab, while currently approved for the treatment of UC in the United States, are not currently approved for the treatment of CD. Some embodiments of the method involve performing an intervention that is effective to treat UC, but either ineffective to treat CD or not yet approved by regulatory authorities for the treatment of CD.

Suitable medical treatments for CD include the administration of pharmaceutical agents or salts thereof. Suitable pharmaceutical agents include: an oral 5-aminosalicylate, such as mesalamine; a vitamin supplement, such as a vitamin B-12 supplement and a vitamin D supplement; a mineral supplement, such as a calcium supplement; an anti-inflammatory; a corticosteroid such as prednisone and budesonide; an immunosuppressant such as azathioprine, tacrolimus, methotrexate, and mercaptopurine; an anti-TNF-α antibody, such as infliximab, adalimumab, and certolizumab pegol; an anti-α-4-integrin antibody, such as natalizumab and vedolizumab; an anti-interleukin antibody, such as ustekinumab; and an antibacterial antibiotic, such as metronidazole, and ciprofloxacin. Although certolizumab pegol, methotrexate, and natalizumab are approved in the US for the treatment of CD, they are not currently approved for the treatment of UC. Surgical approaches are sometimes used to treat severe cases of CD. Such surgeries include ostomy, colostomy, ileostomy, bowel resection, colectomy, proctocolectomy, and strictureplasty. In some embodiments of the method, the subject is treated using a diet that is advantageous for the management of CD, but not necessarily advantageous in the management of UC. One such diet is a low fat diet. Some embodiments of the method involve performing an intervention that is effective to treat CD, but either ineffective to treat UC or not yet approved by regulatory authorities for the treatment of UC. The intervention may be administration of a drug, to the exclusion of a surgery. The administration of a drug may be administration of a drug selected from the group consisting of: a vitamin supplement, an anti-inflammatory, a corticosteroid, prednisolone, methyl-prednisolone, oral budesonide, a 5-aminosalicylate, an immunosuppressant, azathioprine, mercaptopurine, an anti-TNF-alpha antibody, infliximab, adalimumab, certolizumab pegol, methotrexate, an anti-α4-integrin antibody, natalizumab, vedolizumab, an anti-interleukin antibody, ustekinumab, an antibacterial antibiotic, ciprofloxacin, metronidazole, an anticholinergic agent, propantheline, dicyclomine, hyoscyamine, a bile acid sequestrant, cholestyramine, colestipol, and colesevalm. The administration of a drug may be administration of a drug, vitamin, or mineral selected from the group consisting of: vitamin B12, vitamin D, calcium, certolizumab pegol, methotrexate, and natalizumab. The intervention may be enteral nutrition therapy, including elemental and non-elemental diets, such as by nasogastric tube feeding. In an embodiment, the level of DEFA5 or DEFA5 expression may be elevated above normal levels in patients who are likely to be diagnosed UC but, at the time the DEFA5 or DEFA5 expression level is measured, diagnosed as having IC. These patients may be treated with any suitable medical treatments for UC. The intervention may be placing the subject on a low fat diet or a high fiber diet.

The intervention suitable for UC may be administration of a drug selected from the group consisting of: an iron supplement, an anti-inflammatory, a corticosteroid, hydrocortisone, cortisone, prednisolone, a 5-aminosalicylate, an immunosuppressant, azathioprine, mercaptopurine, cyclosporine, an anti-TNF-alpha antibody, infliximab, adalimumab, golimumab, methotrexate, an anti-α4-integrin antibody, vedolizumab, an antibacterial antibiotic, ciprofloxacin, metronidazole, suppository mesalazine, enema mesalazine, olsalazine, balsalazide, enema budesonide, tacrolimus, and a combination of any of the foregoing. The intervention suitable for UC may be administration of a drug selected from the group consisting of: cyclosporine, and golimumab.

A kit is provided for measuring DEFA5 in a subject. The kit may find use in several of the methods provided above, as well as others. The kit may be, for example, used for the diagnosis of inflammatory bowel disease. The kit comprises an assay for measuring at least one of DEFA5 concentration and DEFA5 expression. The kit may include an assay comprising an anti-DEFA5 antibody; and a sample container configured to contain a sample selected from: a stool sample, a blood sample, a bowel tissue sample, and a serum sample. The first assay may include a sample collector selected from the group consisting of: a stool sample collector, a blood sample collector, a serum sample collector, and a bowel tissue collector.

FIG. 1 illustrates dot blotting of the specificity of commercially available DEFA5 antibodies to purified HD1-HD6 proteins versus a Ponceau S control. It is believed that the targeted DEFA5 antibody of the present embodiments has a higher specificity than these commercially available antibodies such that, for example, purification of DEFA5 in samples would not be required or be minimal. As used herein, the term “specificity” or similar terms, used in the context of an antibody regarding to its target, refers to the antibody specifically binding to the target antigen (as opposed to other antigens, such as HD1, HD2, HD3, HD4, and HD6). This higher DEFA5 specificity of the present antibody would allow, for example, easier and more accurate testing of DEFA5 levels or expression in samples from subjects.

FIG. 2A illustrates an alignment of the primary sequence of DEFA5 with that of HD1 and HD6. FIG. 2B is a schematic showing DEFA5 antibody epitopes to distinguish pro-DEFA5 from mature protein in sera of IBD patients. FIG. 2C is a model of sandwich ELISA to be used to detect pro-DEFA5 and mature DEFA5 in sera of IBD patients. FIGS. 3A and 3B illustrate the problem of diagnostic uncertainty and inaccuracy in IBD clinical setting. FIG. 3A shows that twenty-one IC patients were followed for approximately ten years. At the end of the 10 year period, 28.5% of the patients could still not be delineated into a precise diagnosis of either UC or CC. FIG. 3B shows sixty-seven UC RPC operated patients that were followed for re-evaluation after a mean follow-up of 9.4 (range, 8-13) years after operation. Thirty percent of these patients required a change of diagnosis to de novo Crohn's disease.

FIGS. 4A-4D show that DEFA5 levels can be used to determine patient candidacy for IPAA. FIG. 4A shows representative results from a RPC-operated patient that did not change the diagnosis after surgery and was molecularly tested using DEFA5 IHC. FIG. B shows representative results from a UC RPC and IPAA operated patients that did change the diagnosis from UC to de novo Crohn's was molecularly tested using DEFA5 IHC. FIG. 4C shows NL-Ileum, control. FIG. 4D shows quantification of NEARAS DEFA5 IHC staining spot counts for UC RPC and IPAA-operated patients who did not have their original diagnosis changed versus those who did change from UC to de novo Crohn's. (Ctrl 1—staining control, UC—Ulcerative Colitis, CC—Crohn's Colitis, DV—Diverticulitis, DVL—Diverticulosis).

FIGS. 5A-5I illustrate histological staining on parallel sections for the typical morphological appearance of Paneth cell (PCs) including the presence of dense apical eosinophilic granules. Upper panel: FIG. 5A, Diverticulitis (DV, no PCs), FIG. 5B, Diverticulosis (DVL, no PCs), FIG. 5C, Normal (NL-Colon, Control, no PCs).

Middle panel: FIG. 5D, UC (found prodromal PC in one patient, arrow). FIG. 5E, CC, demonstrate abundance of PCs allover colonic basal crypts (arrows). FIG. 5F, Normal (NL-Ileum, Control), with abundance of PCs. Lower panel: IHC detection of Paneth cell markers α-defensin 5 (DEFA5) and lysozyme (LYZ) in the colon. FIG. 5G, NL-Colon, FIG. 5H, CC, and FIG. 5I, NL-Ileum, Control.

FIGS. 6A-6J illustrate H&E staining on parallel sections for the typical morphological appearance of Paneth cell (PCs) including the presence of dense apical eosinophilic granules. Upper panel: FIG. 6A, Diverticulitis (DV, no PCs), FIG. 6B, Diverticulosis (DVL, no PCs), FIG. 6C, Normal (NL-Colon, Control, no PCs). Middle panel: FIG. 6D, UC (found prodromal PC in one patient, arrow). FIG. 6E, CC, demonstrate abundance of PCs allover colonic basal crypts (arrows). FIG. 6F, Normal (NL-Ileum, Control), with abundance of PCs. Lower panel: IHC detection of Paneth cell markers α-defensin 5 (DEFA5) and lysozyme (LYZ) in the colon. FIG. 6G, NL-Colon, FIG. 6H, CC, and FIG. 6I, NL-Ileum, Control.

FIGS. 7A-7J show a double stain of PCs, Lysosomes and DEFA5. Double staining analyses from de novo Crohn's (FIGS. 7A and 7D), and normal ileum/control (FIG. 7G) are illustrated. Image deconvolutions are displayed vertically to evaluate lysozyme specific permanent red (FIGS. 7B, 7E, and 7H) and DEFA5α-specific DAB (FIGS. 7C, 7F, and 7I). The normal colon image (FIG. 7J), which lacks PCs, was not further processed by double staining.

Working Example 1

Working Example 1 shows that human UC and CC can be distinguished molecularly by examining DEFA5 levels in colectomy tissues, colon biopsies, and/or sera in humans using the DEFA5 antibodies described herein. Also, Working Example 1 delineates the underlying mechanisms for the subtle differences between UC and CC. The ability to accurately distinguish CC from UC is significant and of clinical importance, and is especially meaningful for gastroenterologists and colorectal surgeons, particularly before deciding whether restorative proctocolectomy surgery is required in a patient having IBD.

Methods

The inability to accurately distinguish Crohn's disease (CC) from UC leads to an inexact diagnosis denoted as IC, which greatly affects the medical and surgical care of the patients. A preliminary assessment of DEFA5 expression was performed in a pilot cohort of IC patients as well as in UC patients who underwent RPC surgery. This showed that DEFA5 levels and to a lesser extent DEFA6 levels were higher in CC patient samples. The preliminary data reveal that detection of DEFA5 in the tissues of the IC patients or those from the RPC surgery UC patients, who in fact were CC, were more accurately differentiated CC from UC in then otherwise misdiagnosed patients.

Clinical Samples.

To show that aberrant DEFA5 expression in IBD patients is a more reliable diagnostic approach to differentiate CC from UC, the potential of detection of DEFA5 as a biomarker for CC in IBD patient samples diagnosed as UC, CC and IC tissues was explored. FIGS. 11A and 11B illustrate a distribution of collected fresh frozen tissue and blood samples from IBD and none-IBD patients by sex and race. FIG. 11A illustrates a categorization of tissue samples by female, male, white, and black shows tissue samples (732 samples) and FIG. 11B illustrates a categorization of sera samples (186 samples) as female, male, white, and black. The samples were stored at −80° Celsius. The patient samples diagnosed as UC, CC, and IC tissues were subjected to immunohistochemistry (IHC) and semi-quantitative RT-PCR to evaluate the potential for detection of DEFA5 as a biomarker for CC in IBD patient samples diagnosed as UC, CC and IC tissues. A total of 732 tissues and 186 sera from IBD and healthy individuals distributed by race and gender were collected, as depicted in FIGS. 11A and 11B. The tissues were surgical colectomy tissues from consented adults with definitive and unambiguous diagnoses of UC and CC as well as from those diagnosed with IC at Vanderbilt University Medical Center (VUMC). The collection of these patient samples was approved by Meharry Medical College (MMC) and VUMC IRB Committees. The full thickness of the tissues was analyzed by pathology teams at MMC and VUMC following established criteria for IBD subtypes. For each sample, medical data pertaining to patient demographics, variables prior to and after surgery, surveillance endoscopic and clinical findings, and medical and surgical treatment history were reviewed retrospectively. The experimental samples were taken from various parts of the colon.

Clinical Retrospective Studies on IBD Patients Reveal Persistent Diagnostic Uncertainty.

A retrospective investigation was conducted on a cohort of 21 patients diagnosed with IC between 2000 and 2007 at the IBD Center at VUMC, with a mean follow-up period of 8.7±3.7 (range, 4-14) years. In 2014, these patients were re-evaluated to determine whether the diagnosis resolved to UC or CC. Three GI pathologists blinded to the initial clinical outcome re-evaluated each patient and the new diagnosis was presented as a consensus among the attending physicians. The pathology reevaluations concluded that the diagnosis of 6 patients, (28.5%) remained as IC because these could still not be delineated into UC or CC. Meanwhile 43% and 28.5% resolved into UC and CC respectively (FIG. 3A). In another retrospective study, 120 patients with “definitive” UC underwent RPC with IPAA surgery between 2001 and 2008. Of the 120 patients, 67 had their diagnosis reevaluated after a mean follow-up up period of 9.4 (range, 8-13) years with functionally acceptable pouches. As shown in FIG. 3B, 30% of the initial UC diagnosis changed to de novo Crohn's disease (de novo CD). Together, this emphasizes the persistent diagnostic uncertainty of the at least 30% of IBD cases and more so the need for more reliable diagnostic procedures.

Differential Expression of DEFA5 in CC and UC.

Two approaches were used, training and Independent test sets, to identify genes or their products that are differentially expressed in UC versus CC. In a training test set, a whole-transcriptome microarray was performed using RNA extracted and pooled from full-thickness colon samples from UC and CC patients (n=5) using the Affymetrix gene expression array according to the manufacturer's instructions (Affymetrix, Santa Clara, Calif.). Tissues from diverticulitis were used as control. This analysis showed a total of 484 genes that were up- or down-regulated antimicrobial peptides, and mucins between the two diseases. In a test set analysis using microarray technologies (Affymetrix, Santa Clara, Calif.). DEFA5 levels increased the most: 31-fold in CC vs. UC (p<7.23E-05), Table 2. In an independent test set, the gene expression profiling was independently verified using a PCR array (NanoString Technologies Inc., Seattle, Wash.) that specifically targeted inflammatory genes. It was found that DEFA5 was also increased 118-fold in CC vs. UC (p<0.001) in different colon samples from UC and CC patients with same disease activity as in test set. Table 3. The only gene to show up in both the microarray and the PCR array was DEFA5. Among the upregulated genes were α-defensin-5, other antimicrobial peptides, and mucins (Table 2). HD5 was increased the most: 31-fold in CC vs. UC (in a previous test HD5 increase by 118-fold in CC versus UC—Table 3). A full list of the microarray results can be found in Table 2. Table 2 shows a list of targets from an AFFYMETRIX cDNA microarray. A total of 484 genes were highlighted in the microarray as potential markers for distinguishing UC from CC. The gene showing the largest fold change between the two diseases was Human Defensin 5 (HD5).

To further validate these data, DEFA5 expression was assessed by semi-quantitative RT-PCR using RNA extracted from moderate CC and moderate UC tissues (n=3). This analysis confirmed that DEFA5 mRNA levels were significantly higher in CC compared to UC (FIG. 7A, SEM, p<0.03). Dot blotting was used to screen commercially available antibodies against recombinant DEFA5 using bacterial lysates prepared from DEFA1-6 transformed bacteria. This led to the discovery of a monoclonal antibody from Santa Cruz Biotechnology, Inc. (Santa Cruz, Calif.)—α-defensin 5 antibody (catalogue #53997)—as a high specificity and high affinity DEFA5 antibody for use in assays. Next, DEFA5 expression was assessed by western blotting (n>10 for each disease) (FIG. 7B), and it was found that tissues from moderate and severe CC patients expressed higher levels of DEFA5 compared to those from all other disease states (FIG. 7C, p<0.0001). However, because full-thickness samples were used for the western blots, the overall abundance of DEFA5 in the samples was low. Finally, the expression of DEFA5 was examined in moderate IBD and control tissues by IHC using FFPE sections. This analysis also revealed that DEFA5 levels higher in CC tissues (FIG. 7G) than in DV, UC, and normal (NL) control tissues (FIGS. 7D, 7E, and 7F). Quantification of the DEFA5 IHC staining revealed a 5.6-fold increase of DEFA5 in CC vs. UC samples (FIG. 7H, p<0.0001). Interestingly, detection of DEFA5 by IHC depicted localized DEFA5 staining in the base of individual colonic crypts. FIGS. 7A-7H show that DEFA is aberrantly expressed in IBD. FIG. 7A shows quantification of DEFA5 transcript levels in moderate UC and CC samples by semi-quantitative RT-PCR confirms higher DEFA5 levels in moderate CC than in moderate UC (p<0.05). FIG. 7B is a representative DEFA5 western blot showing higher DEFA5 levels in moderate and severe CC compared to all other IBD disease states. β-actin was used as the loading control. FIG. 7C shows a graphical representation (densitometry) of DEFA5 levels in various IBD disease states. Each dot represents the ratio of DEFA5 to β-actin. Moderate and severe CC levels of DEFA5 are both significantly higher than all other disease states (p<0.0001). FIGS. 7D-7H illustrate representative IHC staining of DEFA5 in colonic tissues using formalin-fixed paraffin-embedded (FFPE) thin sections—FIG. 7D shows Diverticulosis, no primary antibody control; FIG. 7E shows moderate diverticulitis; FIG. 7F shows moderate UC; FIG. 7G shows moderate CC; and FIG. 7H shows quantification level of DEFA5 IHC staining in moderate UC vs. moderate CC. Levels of DEFA5 are increased in CC as compared to UC (p<0.0001). Magnification of these illustrated tissues is at 40×.

Detection of DEFA5 in IBD Colectomy Tissues Agrees with Follow-Up Clinical Patient Outcomes as a Potentially Selective Diagnostic Tool for CC.

To test if detection of DEFA5 could be used to discriminate CC from UC and if this agreed with the patient follow-up clinical outcomes, detection of DEFA5 was carried out in the tissues from the 21 IC patients (FIG. 3A) by IHC. The staining intensity was evaluated using the Nikon Element Advanced Research Analysis Software (NEARAS). Based on the DEFA5 staining intensity, it was found that among the six patients with unchanged IC diagnoses, and as depicted in Table 1, below, three patients showed high DEFA5 staining and conformed to the final diagnosis for CC (red circle), and three patients showed low DEFA5 staining and conformed to the final diagnosis for UC (green circle).

DEFA5 staining was also evaluated for the RPC and IPAA-operated patients described in FIG. 3B who had a clinical change in diagnosis to de novo CD (n=20) and those whose diagnoses did not change (n=47). FIG. 4 illustrates how DEFA5, as disclosed herein, is a tool for determining patient candidacy for IPAA. FIG. 4A shows colectomy tissue from an RPC-operated patient whose diagnosis did not change. The tissue was molecularly tested using DEFA5 IHC. FIG. 4B shows colectomy tissue from a UC RPC and IPAA-operated patient whose diagnosis changed from UC to de novo CD. The tissue was molecularly tested using DEFA5 IHC. FIG. 4C shows NL-Ileum, control. FIG. 4D shows quantification to compare NEARAS DEFA5 IHC staining in tissues from UC RPC and IPAA-operated patients whose original diagnoses did not change vs. those whose diagnoses changed from UC to de novo CD (FIG. 11B). (Ctrl 1—control, UC—Ulcerative Colitis, CC—Crohn's Colitis, DV—Diverticulitis, DVL—Diverticulosis). The DEFA5 IHC revealed that patients whose diagnosis remained unchanged i.e. UC, showed only trace levels of DEFA5 (FIGS. 4A and 4D) while those whose diagnoses clinically changed from UC to de novo CD showed significantly strong (p<0.0001) DEFA5 staining (FIGS. 4B and 4D). As expected, DEFA5 staining in normal ileum control tissues was high (FIG. 4C). Statistical analysis to determine positive predictive values (PPVs) of DEFA5 in patient tissues showed 95.8% for CC and only 76.9% for UC. Chi squared analysis shows significant relatedness between high levels of DEFA5 and a CC diagnosis (p<0.0001). These data indicate that DEFA5 is a candidate diagnostic marker to accurately distinguish CC from UC and to reliably reclassify IC into the CC and UC subtypes.

Establish the Specificity, and Selectivity of DEFA5 Antibodies.

Although the detection of DEFA5 in IBD tissues by IHC (FIGS. 4A-4D) is consistent with the RT-PCR data (FIGS. 7A-7H), the commercially available antibodies may exhibit some cross reactivity, especially with PC derived DEFA6. This led us to evaluate commercially available DEFA5 antibodies by dot blotting. A DEFA5 antibody from Santa Cruz Biotechnology (α-defensin 5 antibody catalog number sc-53997) was identified as a DEFA5 specific antibody. An evaluation of the antibody for cross-reactivity with DEFA6 revealed that this antibody strongly detected DEFA5 and to a lesser extent DEFA6 (FIG. 10A). Given the possibility that antibodies to these proteins may cross-react, it was sought to identify DEFA5 specific antibodies. A total of 11 monoclonal antibodies to DEFA5 were obtained from R&D Systems and their ability to be used as specific DEFA5 detection antibodies was evaluated (FIG. 10C). A DEFA5 sandwich ELISA kit (OKEH01234) was obtained from AVIVA System Biology Inc. to determine whether DEFA5 can be detected in patient sera. Surprisingly, DEFA5 was detected in sera from profiled patients with mild CC and mild UC activity and found that DEFA5 was higher in sera from CC than in UC patients, p<0.05; R2=0.9938 (FIG. 10B).

Prophetic Example 2

Establish the Specificity, and Selectivity of DEFA5 Antibodies for Sandwich ELISAs.

It is believed that the specificity of the commercially available ELISA kit can be determined by using DEFA6 as the antigen. If test proves to be not specific, it is believed that immunoprecipitations (IPs) using DEFA5 and DEFA6 expressed in bacteria and the 11 monoclonal antibodies to DEFA5 can identify those that may specifically form immune complexes with DEFA5 but not DEFA6 can be conducted. It is believed that a R&D Systems DEFA5 antibody (catalogue number 972207.111 or CSL 1450400) from R&D SYSTEMS, Minneapolis, Minn., can be biotinylated and used as the detection antibody for the IPs. It is believed that the combination of the detection and the best capture antibodies to develop a more specific sandwich ELISA to detect DEFA5 in sera. Overall, it is believed that purified DEFA5 expressed in bacteria can be used to determine the appropriate concentrations of the DEFA5 antibodies for a robust ELISA and compare this with the commercially available ELISA kits.

Optimize the DEFA5 Sandwich ELISA to Detect DEFA5 in Sera from IBD Patients and Normal Subjects.

Since DEFA5 has not been used in IBD clinical settings, the goal of this task will be to establish normal blood DEFA5 reference interval levels and compare these to the values in sera of IBD patients. As depicted in FIG. 10B, it is envisioned that DEFA5, a protein produced locally at the intestinal mucosal crypt, can be detected in circulating human sera by sandwich ELISA. Sera from 117 IBD patients (40 UC, 52 CC, and 25 IC) and 69 non-IBD controls across different race/ethnicities and both genders (FIG. 11B) has been collected. A sample size of 92 subjects, (46 CC and 46 UC) will be used to detect a clinically significant difference of 19% between the positive predictive values of CC and UC using a one-tailed test of proportions between the two groups with 80% statistical power and a 5% level of significance. This 19% difference represents a 96% probability that subjects in CC group with a positive screening test truly have the disease and the 77% positive predictive value for subjects in UC group. To establish normal values of DEFA5 in human sera, up to 120 sera from males and a similar number from females with varied ethnic backgrounds, from outpatient clinics at MMC and VUMC will be used. Sera will be disqualified from those who have been diagnosed with diseases that may impact the analysis. Pre-analytical sampling and quantitative analysis will be performed, as well as the definition, establishment, and verification of DEFA5 reference intervals according to previously established guidelines. Blood samples from healthy individuals at VUMC Clinical Research Center (CRC) at Clinical Chemistry Pathology Laboratories, which is part of the Vanderbilt Institute for Clinical and Translational Research (VICTR), will be analyzed. The additional blood samples will be consented to and collected from healthy adult volunteers and from IBD patients as an ongoing process to add to the serum collection (FIG. 11B).

Detect DEFA5 Expression in Formalin-Fixed, Paraffin-Embedded (FFPE) IBD Biopsies/Tissues by IHC.

205 FFPE blocks were collected from IBD patients during a prior R21 funding period. Of these samples, 83 are from UC, 75 are from CC, and 47 are from IC patients. Tissues from DV patients will be used as non-IBD controls. The thin FFPE sections from these samples will be stained with anti-DEFA5 antibody at the Translational Pathology Shared Resource (TPSR). Following IHC staining, the slides will be digitally scanned using the Ariol SL-50 digital high resolution imaging system (Leica) and quantified using the Tissue IA software at the Digital Histology Shared Resource (DHSR) at Vanderbilt University. This will enable the scoring for each slide based on its staining intensity and percentage of stained cells. This digital analysis of IHC results will serve as either an additional or an alternative bioassay for DEFA5 detection in biopsies.

Determine Whether Differences in the Levels of DEFA5 in the Colonic Mucosa Tissues Correlate with Circulating Levels of DEFA5 in CC, UC or Normal Subjects.

To determine whether the level of circulating or secreted DEFA5 (sDEFA5) correlates with its level of expression in situ, biopsy samples collected from the three groups will be used to isolate mRNA to determine by real time PCR the levels of DEFA5 message present. If possible, simultaneous biopsies from areas of CC activity vs. normal, adjacent tissue will inform us regarding whether serum levels denote active disease. To that end, biopsy specimens from normal, adjacent mucosal, actively inflamed mucosa, and mucosa around the transitional zone will be examined for DEFA5 mRNA expression. A power analysis indicates that comparison of prevalence between case and control groups having 30 subjects per group would generally have 84% power to detect 40% differences (e.g. 40% vs. 80%, odds ratio 6.0) based on a two-sided test with 0.05 alpha level. In terms of precision for the prevalence estimates, when the sample size of each group is 30, a two-sided 95% confidence interval for a single proportion will be 18% from the observed rate expected to be 50%. Sample size requirements were calculated based on detecting differentially expressed proteins between two groups while controlling for the false discovery rate (FDR). The measure is the ratio of protein expression (or fold) in cases to controls for a particular protein. Effect sizes equal to 1.5 fold change with more than 80% power can be detected, based on algorithms from Jung S H, Bioinformatics 2005; 21:3097. This assumes a FDR of 0.001 and two-sided p-values, and is based on a sample of 30 cases and 30 controls. To determine the significance of sDEFA5 as a candidate biomarker of active CC and achieve a model with predictive accuracy, the models such as generalized linear model with regularization approaches and ensemble methods for feature identification including boosting, bagging, and random forest classifier will be used.

Anticipated Results, Challenges, and Alternative Procedures.

It is believed that DEFA5 specific assays to detect DEFA5 in sera and tissues of IBD patients will be shown. With this, quantitative standard numerical normal reference interval (RI) values can be determined and developed for DEFA5 in sera from healthy subjects and relate these to the levels in IBD patient sera. The RI approach will be based on the central 95% of laboratory test values observed for a reference population that is free of diseases. Based on the preliminary data, it is anticipated that DEFA5 expression will be higher in tissues and sera from CC patients than in those from UC patients and that all patients with IC can be reclassified as either CC or UC patients. Although the power calculation indicated 46 patients per disease subtype, up to 100 patient tissues and sera per disease will be used from varied ethnic backgrounds to validate the detection of DEFA5 as a diagnostic tool for CC in sera.

While it is possible that the sensitivity of the assays may be poor due to relatively low levels of DEFA5 in sera, the assays will be validated by using alkaline phosphatase-conjugated anti-DEFA5 monoclonal antibodies or modify the assay to direct ELISA or a radioimmunoassay. Peroxidase-conjugated streptavidin can be used to develop a DEFA5 detection assay using 2,2′-Azinobis [3-ethylbenzothiazoline-6-sulfonic acid]-diammonium salt (ABTS) as a substrate. It is believed that the development of a sandwich assay and the antibodies will avoid cross reaction with DEFA6.

Working Example 3

Paneth cells are the differentiated progenies of the ileal epithelial stem cells (ISCs) that support the ISCs and provide antibacterial protection in mammals. Although IBD is inflammation prone, the notion that UC and CC are histologically different and require distinct surgical treatment options suggests that DEFA5 and/or specific pro-inflammatory cytokines play a major role in the pathogenesis of these diseases. It is believed that the high levels of DEFA5 in CC colectomy samples arise from aberrant metaplastic colonic crypt PCs; and that sera from patients with UC and CC contain high levels of IBD subtype specific pro-inflammatory cytokines. There is ample evidence supporting the possibility that bacterial enterotoxins such as Staphylococcal enterotoxin C and cholera toxin (Xiao-Chen Wan et al., 2008, Androutsellis-Theotokis A et al., 2011), and that pro-inflammatory cytokines such as TNF-α, IL-1β, and IFN-γ (Valdez I A et al., 2016) promote the differentiation of stem cells. However, whether bacterial enterotoxins or pro-inflammatory cytokines with or without and DEFA5 underlie the distinct pathologic features of CC relative to UC remain poorly understood. It is believed that DEFA5, bacterial enterotoxins and/or certain CC-associated pro-inflammatory cytokines promote the differentiation/expansion of colonic stem cells, and the distinct pathology associated with CC. To test this hypothesis, and in the absence of de facto animal models for CC, two different normal human colonic epithelial cell lines (NCM460 and NCM356), colonoids and/or enteroids from endoscopy biopsy tissues will be used to a) test the effects of purified DEFA5, DEFA6, and DEFA1 in the presence or absence of bacterial enterotoxins on the formation of metaplastic colonic PCs; b) assess the effects of CC- and UC-specific cytokines on DEFA5 secretion, the generation of ROS and cell viability. It is believed that DEFA5 and, to a lesser extent, DEFA6 will promote the secretion of CC-specific cytokines and the production of ROS, but attenuate both cell viability and tissue damage. It is also believed that the CC-specific cytokines will promote the synthesis/secretion of DEFA5 while the UC-specific cytokines will have the opposite effects.

Aberrantly expressed DEFA5 in CC patients is synthesized by metaplastic colonic crypt PCs. DEFA5 is predominantly synthesized by PCs. Therefore, it was determined whether PCs were present in the colon crypt of CC patients and to validate whether the pool of DEFA5 found in CC and in de novo CD colectomy samples originated from colonic epithelial crypts. All 20 UC samples from RPC-operated patients with de novo CD showed pools of colonic metaplastic crypt PCs, as demonstrated by H&E staining (FIGS. 8A-8C). IHC staining of lysozymes in PCs confirmed the abundance of PCs in CC colonic crypts than those in UC (FIGS. 8D-8F, arrows). FIGS. 8A-8C illustrate Representative H&E staining of colonic resected tissues. 8A, Normal colon (NLC). 8B, UC, sporadic PC (arrow). 8C, CC, with mature PCs in the crypts, (arrows). FIGS. 8D-8F illustrate representative IHC detection of DEFA5 and lysozyme in the colon. 8D, NLC. 8E, UC, (sporadic prodromal PC in one patient). 8F, CC. Magnification was at 40×.

It was found that the PCs were the DEFA5 secreting cells by staining the colectomy tissue samples for DEFA5 and lysozyme (LYZ) to detect PCs. It was found that abundant crypt PCs were present in CC samples (FIGS. 6A & 6D). Normal ileal tissues were used as control (FIG. 6G). FIGS. 6A-6I illustrate that DEFA5 and lysozyme are co-expressed in crypt PCs in CC. Double staining of de novo Crohn's tissues from two patients (6A and 6D), and normal ileum (control) (6G) with lysozyme (6B, 6E & 6F) and with DEFA5 (6C, 6F, & 6I). Merged images are shown in 6A, 6D & 6G). To ascertain that the PCs were the DEFA5 secreting cells, the colectomy tissue samples were stained for DEFA5 and lysozyme (LYZ) to detect PCs. Abundant crypt PCs were found in CC samples (FIGS. 6A & 6D). Normal ileal tissues were used as control (FIG. 6G).

FIGS. 9A-9D illustrate the presence of DEFA5 in adjacent IBD tissues. IHC and H&E staining of DEFA5 in adjacent normal and diseased tissues from CC patients (9A and 9B) and from UC patients (FIGS. 9C and 9D). Note that DEFA5 staining is not obvious in the disease and normal tissues from UC patients. DEFA5 is detected in adjacent normal tissues from CC. Given that normal healthy colon tissues lack or have scanty PCs, it was sought to determine if DEFA5 could be detected in the normal tissues adjacent to the diseased tissues in CC and UC patients. IHC for DEFA5 shows positive staining in the base of the crypts in both the inflamed and normal adjacent tissues in samples from CC patients (FIG. 9A). FIG. 9B depicts H&E. Given the co-localization of DEFA5 and PCs (FIG. 6), it is plausible to suggest that PCs are present in the diseased and normal adjacent tissues of CC patients but not in tissues from UC patients. However what triggers the appearance of PCs in this IBD disease subtype remains poorly understood.

It is to be understood that any given elements of the disclosed embodiments of the invention may be embodied in a single structure, a single step, a single substance, or the like. Similarly, a given element of the disclosed embodiment may be embodied in multiple structures, steps, substances, or the like.

The foregoing description illustrates and describes the processes, machines, manufactures, compositions of matter, and other teachings of the present disclosure. Additionally, the disclosure shows and describes only certain embodiments of the processes, machines, manufactures, compositions of matter, and other teachings disclosed, but as mentioned above, it is to be understood that the teachings of the present disclosure are capable of use in various other combinations, modifications, and environments and are capable of changes or modifications within the scope of the teachings as expressed herein, commensurate with the skill and/or knowledge of a person having ordinary skill in the relevant art. The embodiments described hereinabove are further intended to explain certain best modes known of practicing the processes, machines, manufactures, compositions of matter, and other teachings of the present disclosure and to enable others skilled in the art to utilize the teachings of the present disclosure in such, or other, embodiments and with the various modifications required by the particular applications or uses. Accordingly, the processes, machines, manufactures, compositions of matter, and other teachings of the present disclosure are not intended to limit the exact embodiments and examples disclosed herein. Any section headings herein are provided only for consistency with the suggestions of 37 C.F.R. § 1.77, or otherwise to provide organizational queues. These headings shall not limit or characterize the invention(s) set forth herein.

TABLE 2 Gene Gene p-value Fold Information Symbol RefSeq (CC vs UC) Increase NM_021010 // DEFA5 // defensin, alpha 5, DEFA5 NM_021010 7.23E−05 31.0374 Paneth cell-specific // 8p23.1 // 1670 NM_002909 // REG1A // regenerating islet- REG1A NM_002909 0.00321456 21.9439 derived 1 alpha // 2p12 // 5967 /// ENS NM_138938 // REG3A // regenerating islet- REG3A NM_138938 0.000310891 17.3268 derived 3 alpha // 2p12 // 5068 /// NM_(—) NM_001926 // DEFA6 // defensin, alpha 6, DEFA6 NM_001926 0.0024893 16.139 Paneth cell-specific // 8p23.1 // 1671 NM_058186 // FAM3B // family with FAM3B NM_058186 0.00116588 14.6887 sequence similarity 3, member B // 21q22.3 // NM_006507 // REG1B // regenerating islet- REG1B NM_006507 0.0120953 13.9675 derived 1 beta // 2p12 // 5968 /// ENST NM_001074 // UGT2B7 // UDP UGT2B7 NM_001074 0.0154146 9.92532 glucuronosyltransferase 2 family, polypeptide B7 // 4 NM_001285 // CLCA1 // chloride channel CLCA1 NM_001285 0.00297816 9.07579 accessory 1 // 1p22.3 // 1179 /// ENST000 NM_003122 // SPINK1 // serine peptidase SPINK1 NM_003122 0.007176 7.60063 inhibitor, Kazal type 1 // 5q32 // 6690 NM_001076 // UGT2B15 // UDP UGT2B15 NM_001076 0.0169187 7.12294 glucuronosyltransferase 2 family, polypeptide B15 // NM_001076 // UGT2B15 // UDP UGT2B15 NM_001076 0.0169187 7.12294 glucuronosyltransferase 2 family, polypeptide B15 // NM_000343 // SLC5A1 // solute carrier SLC5A1 NM_000343 0.00447091 7.0494 family 5 (sodium/glucose cotransporter), m NM_000134 // FABP2 // fatty acid binding FABP2 NM_000134 0.0300574 6.63756 protein 2, intestinal // 4q28-q31 // 21 NM_000035 // ALDOB // aldolase B, ALDOB NM_000035 0.0444145 6.30502 fructose-bisphosphate // 9q21.3-q22.2 // 229/ NM_002770 // PRSS2 // protease, serine, 2 PRSS2 NM_002770 0.0052665 6.27999 (trypsin 2) // 7q34 // 5645 /// ENST00 NM_005379 // MYO1A // myosin IA // MYO1A NM_005379 0.00588172 5.72861 12q13-q14 // 4640 /// ENST00000300119 // MYO1 NM_007329 // DMBT1 // deleted in DMBT1 NM_007329 0.0365636 5.56609 malignant brain tumors 1 // 10q26.13 // 1755 // NM_031457 // MS4A8B // membrane-spanning MS4A8B NM_031457 0.00577952 5.34254 4-domains, subfamily A, member 8B // 11 NM_001041 // SI // sucrase-isomaltase SI NM_001041 0.0417578 5.23854 (alpha-glucosidase) // 3q25.2-q26.2 // 647 NM_000482 // APOA4 // apolipoprotein A-IV // APOA4 NM_000482 0.0468523 5.15957 11q23 // 337 /// ENST00000357780 // NM_006418 // OLFM4 // olfactomedin 4 // OLFM4 NM_006418 0.038931 5.05883 13q14.3 // 10562 /// ENST00000219022 // NM_000482 // APOA4 // apolipoprotein A-IV // APOA4 NM_000482 0.0472178 4.92519 11q23 // 337 /// ENST00000357780 // NM_004133 // HNF4G // hepatocyte nuclear HNF4G NM_004133 0.0113549 4.8964 factor 4, gamma // 8q21.11 // 3174 /// NM_017675 // CDHR2 // cadherin-related CDHR2 NM_017675 0.00253568 4.82206 family member 2 // 5q35.2 // 54825 /// NM NM_005588 // MEP1A // meprin A, alpha MEP1A NM_005588 0.0198087 4.78504 (PABA peptide hydrolase) // 6p12-p11 // 42 NM_002354 // EPCAM // epithelial cell EPCAM NM_002354 0.0242383 4.77321 adhesion molecule // 2p21 // 4072 /// ENST NM_001172312 // PLS1 // plastin 1 // 3q23 // PLS1 NM_001172312 0.0155248 4.73894 5357 /// NM_001145319 // PLS1 // pl NM_002354 // EPCAM // epithelial cell EPCAM NM_002354 0.0297878 4.72533 adhesion molecule // 2p21 // 4072 /// ENST NM_001150 // ANPEP // alanyl (membrane) ANPEP NM_001150 0.0203087 4.58929 aminopeptidase // 15q25-q26 // 290 /// E NM_001077 // UGT2B17 // UDP UGT2B17 NM_001077 0.0267812 4.51157 glucuronosyltransferase 2 family, polypeptide B17 // NM_002591 // PCK1 // PCK1 NM_002591 0.0333639 4.50793 phosphoenolpyruvate carboxykinase 1 (soluble) // 20q13.31 / NM_021804 // ACE2 // angiotensin I ACE2 NM_021804 0.0271919 4.49025 converting enzyme (peptidyl-dipeptidase A) 2 NM_024308 // DHRS11 // dehydrogenase/ DHRS11 NM_024308 0.0176773 4.41914 reductase (SDR family) member 11 // 17q12/ NM_019010 // KRT20 // keratin 20 // KRT20 NM_019010 0.026162 4.35459 17q21.2 // 54474 /// ENST00000167588 // KRT2 ENST00000319509 // MUC3A // mucin 3A, MUC3A ENST00000319509 0.00353785 4.28484 cell surface associated // 7q22 // 4584 // NM_000379 // XDH // xanthine XDH NM_000379 0.00289109 4.17476 dehydrogenase // 2p23.1 // 7498 /// ENST00000379416 NM_007127 // VIL1 // villin 1 // 2q35 // 7429 /// VIL1 NM_007127 0.00825691 4.16925 ENST00000248444 // VIL1 // vil NM_025130 // HKDC1 // hexokinase domain HKDC1 NM_025130 0.00344261 4.13874 containing 1 // 10q22.1 // 80201 /// ENS NR_029578 // MIR192 // microRNA 192 // MIR192 NR_029578 0.00199884 4.12467 11q13.1 // 406967 NM_004063 // CDH17 // cadherin 17, LI CDH17 NM_004063 0.0331015 4.12001 cadherin (liver-intestine) // 8q22.1 // 10 NM_024922 // CES3 // carboxylesterase 3 // CES3 NM_024922 0.0022354 4.11886 16q22.1 // 23491 ///NM_001185177 // NM_033049 // MUC13 // mucin 13, cell MUC13 NM_033049 0.0271079 4.11287 surface associated // 3q21.2 // 56667 /// E NM_000888 // ITGB6 // integrin, beta 6 // ITGB6 NM_000888 0.000602949 4.09738 2q24.2 // 3694 /// ENST00000283249 // NM_004963 // GUCY2C // guanylate GUCY2C NM_004963 0.00645462 4.0793 cyclase 2C (heat stable enterotoxin receptor)/ NM_004293 // GDA // guanine deaminase // GDA NM_004293 0.0208862 4.0739 9q21.13 // 9615 /// ENST00000358399 // NM_001307 // CLDN7 // claudin 7 // 17p13 // CLDN7 NM_001307 0.0213404 4.06183 1366 /// NM_001185022 // CLDN7 // cl NR_033807 // CYP3A5 // cytochrome P450, CYP3A5 NR_033807 0.0046334 4.04376 family 3, subfamily A, polypeptide 5 // NM_021924 // CDHR5 // cadherin-related CDHR5 NM_021924 0.00480695 3.97925 family member 5 // 11p15.5 // 53841 /// N NM_001010922 // BCL2L15 // BCL2-like 15 // BCL2L15 NM_001010922 0.027053 3.96946 1p13.2 // 440603 /// ENST00000393316 NM_020770 // CGN // cingulin // 1q21 // CGN NM_020770 0.00129584 3.94184 57530 /// ENST00000271636 // CGN // cing NM_032787 // GPR128 // G protein-coupled GPR128 NM_032787 0.00779494 3.93937 receptor 128 // 3q12.2 // 84873 /// ENS NM_138933 // A1CF // APOBEC1 A1CF NM_138933 0.00976589 3.79699 complementation factor // 10q11.23 // 29974 /// NM_(—) NM_152311 // CLRN3 // clarin 3 // 10q26.2 // CLRN3 NM_152311 0.0132404 3.74982 119467 /// ENST00000368671 // CLRN3 NM_007072 // HHLA2 // HERV-H LTR- HHLA2 NM_007072 0.0139075 3.74668 associating 2 // 3q13.13 // 11148 /// ENST00000 NM_003399 // XPNPEP2 // X-prolyl XPNPEP2 NM_003399 0.0359348 3.73179 aminopeptidase (aminopeptidase P) 2, membrane-b NM_021258 // IL22RA1 // interleukin 22 IL22RA1 NM_021258 0.00520995 3.72759 receptor, alpha 1 // 1p36.11 // 58985 /// NM_000149 // FUT3 // fucosyltransferase 3 FUT3 NM_000149 0.0106419 3.70158 (galactoside 3(4)-L-fucosyltransferase NM_002644 // PIGR // polymeric PIGR NM_002644 0.0363588 3.68869 immunoglobulin receptor // 1q31-q41 // 5284 /// E NM_001136503 // C19orf77 // chromosome C19orf77 NM_001136503 0.0114867 3.6586 19 open reading frame 77 // 19p13.3 // 28 NR_024626 // C17orf73 // chromosome 17 C17orf73 NR_024626 0.00240775 3.64138 open reading frame 73 // 17q21.33 // 5501 NM_020973 // GBA3 // glucosidase, beta, GBA3 NM_020973 0.0362758 3.63402 acid 3 (cytosolic) // 4p15.2 // 57733 // NM_023944 // CYP4F12 // cytochrome CYP4F12 NM_023944 0.00468827 3.62246 P450, family 4, subfamily F, polypeptide 12/ NM_024320 // PRR15L // proline rich 15-like // PRR15L NM_024320 0.0331566 3.60367 17q21.32 // 79170 /// ENST0000030 NM_005495 // SLC17A4 // solute carrier SLC17A4 NM_005495 0.0299201 3.59753 family 17 (sodium phosphate), member 4 // NM_001135099 // TMPRSS2 // transmembrane TMPRSS2 NM_001135099 0.0351257 3.57585 protease, serine 2 // 21q22.3 // 7113/ NM_001193434 // C10orf81 // chromosome C10orf81 NM_001193434 0.00228381 3.5687 10 open reading frame 81 // 10q25.3 // 79 NM_001935 // DPP4 // dipeptidyl-peptidase DPP4 NM_001935 0.0302652 3.49144 4 // 2q24.3 // 1803 /// ENST0000036053 NM_001644 // APOBEC1 // apolipoprotein B APOBEC1 NM_001644 0.0138008 3.48792 mRNA editing enzyme, catalytic polypept NM_004360 // CDH1 // cadherin 1, type 1, CDH1 NM_004360 0.010781 3.48059 E-cadherin (epithelial) // 16q22.1 // 9 NM_024921 // POF1B // premature ovarian POF1B NM_024921 0.0313161 3.44457 failure, 1B // Xq21.2 // 79983 /// ENSTO NM_002416 // CXCL9 // chemokine (C-X-C CXCL9 NM_002416 0.00248734 3.44146 motif) ligand 9 // 4q21 // 4283 /// ENSTO NM_014479 // ADAMDEC1 // ADAM-like, ADAMDEC1 NM_014479 0.00203661 3.42469 decysin 1 // 8p21.2 // 27299 III NM_00114527 NM_001112706 // SCIN // scinderin // SCIN NM_001112706 0.00493508 3.3952 7p21.3 // 85477 /// NM_033128 // SCIN // sc NR_024345 // NCRNA00262 // non-protein NCRNA00262 NR_024345 0.037473 3.39502 coding RNA 262 // 12q24.31 // 283460 NM_002273 // KRT8 // keratin 8 // 12q13 // KRT8 NM_002273 0.0146545 3.39222 3856 /// ENST00000293308 // KRT8 // k NM_001038603 // MARVELD2 // MARVEL MARVELD2 NM_001038603 0.0179974 3.37682 domain containing 2 // 5q13.2 // 153562 /// E NM_001038603 // MARVELD2 // MARVEL MARVELD2 NM_001038603 0.0179974 3.37682 domain containing 2 // 5q13.2 // 153562 /// E NM_144575 // CAPN13 // calpain 13 // CAPN13 NM_144575 0.013239 3.36885 2p22-p21 // 92291 /// ENST00000295055 // CA NM_022129 // PBLD // phenazine PBLD NM_022129 0.00497915 3.3666 biosynthesis-like protein domain containing // 10 NM_000775 // CYP2J2 // cytochrome P450, CYP2J2 NM_000775 0.0196093 3.36302 family 2, subfamily J, polypeptide 2 // NM_001135195 // SLC39A5 // solute carrier SLC39A5 NM_001135195 0.00623473 3.34227 family 39 (metal ion transporter), mem NM_138788 // TMEM45B // transmembrane TMEM45B NM_138788 0.0306305 3.33725 protein 45B // 11q24.3 // 120224 /// ENSTO NM_176813 // AGR3 // anterior gradient AGR3 NM_176813 0.0400823 3.32266 homolog 3 (Xenopus laevis) // 7p21.1 // 1 NM_022901 // LRRC19 // leucine rich repeat LRRC19 NM_022901 0.0294679 3.31296 containing 19 // 9p21.2 // 64922 /// NM_139053 // EPS8L3 // EPS8-like 3 // EPS8L3 NM_139053 0.00371579 3.29224 1p13.3 // 79574 /// NM_133181 // EPS8L3 // NM_017697 // ESRP1 // epithelial splicing ESRP1 NM_017697 0.0234665 3.27492 regulatory protein 1 // 8q22.1 // 5484 NM_002457 // MUC2 // mucin 2, oligomeric MUC2 NM_002457 0.0182535 3.26416 mucus/gel-forming // 11p15.5 // 4583 // NR_001296 // TRY6 // trypsinogen C // 7q34 // TRY6 NR_001296 0.0203767 3.24356 154754 /// NM_002770 // PRSS2 // p NM_002773 // PRSS8 // protease, serine, 8 // PRSS8 NM_002773 0.0131026 3.2405 16p11.2 // 5652 /// ENST00000317508 NM_025214 // CCDC68 // coiled-coil domain CCDC68 NM_025214 0.00627753 3.2264 containing 68 // 18q21 // 80323 /// NM NM_001943 // DSG2 // desmoglein 2 // DSG2 NM_001943 0.0357587 3.22627 18q12.1 // 1829 /// ENST00000261590 // DSG2 NM_000772 // CYP2C18 // cytochrome CYP2C18 NM_000772 0.0100284 3.20876 P450, family 2, subfamily C, polypeptide 18/ NM_000767 // CYP2B6 // cytochrome P450, CYP2B6 NM_000767 0.00589423 3.19484 family 2, subfamily B, polypeptide 6 // NM_016234 // ACSL5 // acyl-CoA synthetase ACSL5 NM_016234 0.00353915 3.19242 long-chain family member 5 // 10q25.1- NM_145865 // ANKS4B // ankyrin repeat ANKS4B NM_145865 0.027168 3.16823 and sterile alpha motif domain containing NM_032579 // RETNLB // resistin like beta // RETNLB NM_032579 0.0226491 3.14305 3q13.1 // 84666 /// ENST00000295755 NM_021978 // STM // suppression of STU NM_021978 0.0143682 3.14171 tumorigenicity 14 (colon carcinoma) // 11q24 NM_000492 // CFTR // cystic fibrosis CFTR NM_000492 0.0330127 3.13524 transmembrane conductance regulator (ATP-bi NM_018842 // BAIAP2L1 // BA11-associated BAIAP2L1 NM_018842 0.00626097 3.13099 protein 2-like 1 // 7q22.1 // 55971 /// NM_001165958 // GSDMB // gasdermin B // GSDMB NM_001165958 0.0013942 3.1309 17q12 // 55876 /// NM_001042471 // GSDMB NM_024422 // DSC2 // desmocollin 2 // DSC2 NM_024422 0.0115939 3.11862 18q12.1 // 1824 /// NM_004949 // DSC2 // d NM_006017 // PROM 1 // prominin 1 // PROM1 NM_006017 0.0116042 3.10273 4p15.32 // 8842 /// NM_001145847 // PROM1 // NM_017878 // HRASLS2 // HRAS-like HRASLS2 NM_017878 0.0267887 3.09847 suppressor 2 // 11q12.3 // 54979 /// ENST00000 NM_002203 // ITGA2 // integrin, alpha 2 ITGA2 NM_002203 0.00793505 3.07141 (CD49B, alpha 2 subunit of VLA-2 recepto NM_005123 // NR1H4 // nuclear receptor NR1H4 NM_005123 0.0456782 3.06865 subfamily 1, group H, member 4 // 12q23.1 NM_001145862 // MTMR11 // myotubularin MTMR11 NM_001145862 0.00116554 3.03455 related protein 11 // 1q12-q21 // 10903/ NM_018414 // ST6GALNAC1 // ST6 (alpha- ST6GALNAC1 NM_018414 0.0240185 3.0202 N-acetyl-neuraminyl-2,3-beta-galactosyl-1, NM_001080527 // MYO7B // myosin VIIB // MYO7B NM_001080527 0.00130692 2.99927 2q21.1 // 4648 /// ENST00000428314 // MY NM_002153 // HSD17B2 // hydroxysteroid HSD17B2 NM_002153 0.0213389 2.99803 (17-beta) dehydrogenase 2 // 16q24.1-q24. AK095678 // LOC151009 // hypothetical LOC151009 AK095678 0.000466288 2.99502 LOC151009 // 2q13 // 151009 /// AK056084/ NM_000769 // CYP2C19 // cytochrome CYP2C19 NM_000769 0.0193957 2.99186 P450, family 2, subfamily C, polypeptide 19/ NM_000790 // DDC // dopa decarboxylase DDC NM_000790 0.0257511 2.98778 (aromatic L-amino acid decarboxylase) // NM_001143948 // C6orf105 // chromosome C6orf105 NM_001143948 0.0220945 2.95786 6 open reading frame 105 // 6p24.1 // 848 NM_001015001 // CKMT1A // creatine CKMT1A NM_001015001 0.042629 2.95709 kinase, mitochondrial 1A // 15q15 // 548596/ NM_001015001 // CKMT1A // creatine CKMT1A NM_001015001 0.042629 2.95709 kinase, mitochondrial 1A // 15q15 // 548596/ NM_019893 // ASAH2 // N-acylsphingosine ASAH2 NM_019893 0.0167497 2.95643 amidohydrolase (non-lysosomal ceramidase NM_001002236 // SERPINA1 // serpin SERPINA1 NM_001002236 0.0170929 2.94245 peptidase inhibitor, clade A (alpha-1 antipro NM_002031 // FRK // fyn-related kinase // FRK NM_002031 0.0177896 2.93608 6q21-q22.3 // 2444 /// ENST00000368626 NM_001190482 // PCSK5 // proprotein PCSK5 NM_001190482 0.00160967 2.92603 convertase subtilisin/kexin type 5 // 9q21.3 NM_004415 // DSP // desmoplakin // 6p24 // DSP NM_004415 0.0116502 2.91732 1832 /// NM_001008844 // DSP // desmo NM_004591 // CCL20 // chemokine (C-C CCL20 NM_004591 0.0229351 2.91511 motif) ligand 20 // 2q33-q37 // 6364 /// NM NM_000561 // GSTM1 // glutathione S- GSTM1 NM_000561 0.032505 2.91233 transferase mu 1 // 1p13.3 // 2944 /// NM_14 NM_000927 // ABCB1 // ATP-binding ABCB1 NM_000927 0.03279 2.89709 cassette, sub-family B (MDR/TAP), member 1 // NM_000187 // HGD // homogentisate 1,2- HGD NM_000187 0.0180393 2.8961 dioxygenase // 3q13.33 // 3081 /// ENST000 NM_000187 // HGD // homogentisate 1,2- HGD NM_000187 0.0180393 2.8961 dioxygenase // 3q13.33 // 3081 /// ENST000 NM_153676 // USH1C // Usher syndrome USH1C NM_153676 0.00547469 2.88241 1C (autosomal recessive, severe) // 11p14.3 NM_005624 // CCL25 // chemokine (C-C CCL25 NM_005624 0.0492359 2.86049 motif) ligand 25 // 19p13.2 // 6370 /// ENS NM_004174 // SLC9A3 // solute carrier SLC9A3 NM_004174 0.0173616 2.8567 family 9 (sodium/hydrogen exchanger), memb NM_001306 // CLDN3 // claudin 3 // 7q11.23 // CLDN3 NM_001306 0.0490185 2.84657 1365 /// ENST00000395145 // CLDN3 NM_001114309 // ELF3 // E74-like factor 3 ELF3 NM_001114309 0.00265363 2.84098 (ets domain transcription factor, epit NM_000507 // FBP1 // fructose-1,6- FBP1 NM_000507 0.022351 2.83767 bisphosphatase 1 // 9q22.3 // 2203 /// NM_0011 NM_025257 // SLC44A4 // solute carrier SLC44A4 NM_025257 0.0415598 2.83697 family 44, member 4 // 6p21.3 // 80736 // NM_025257 // SLC44A4 // solute carrier SLC44A4 NM_025257 0.0415598 2.83697 family 44, member 4 // 6p21.3 // 80736 // NM_025257 // SLC44A4 // solute carrier SLC44A4 NM_025257 0.0415598 2.83697 family 44, member 4 // 6p21.3 // 80736 // NM_001017970 // TMEM30B // transmembrane TMEM30B NM_001017970 0.00717685 2.83259 protein 30B // 14q23.1 // 161291 /// EN NM_003963 // TM4SF5 // transmembrane 4 TM4SF5 NM_003963 0.0295851 2.82875 L six family member 5 // 17p13.3 // 9032 NM_002242 // KCNJ13 // potassium KCNJ13 NM_002242 0.0400838 2.82471 inwardly-rectifying channel, subfamily J, membe NM_017655 // GIPC2 // GIPC PDZ domain GIPC2 NM_017655 0.0155498 2.81938 containing family, member 2 // 1p31.1 // 5 NM_001127605 // LIPA // lipase A, LIPA NM_001127605 0.000449938 2.81611 lysosomal acid, cholesterol esterase // 10q23. NM_001249 // ENTPD5 // ectonucleoside ENTPD5 NM_001249 0.0118697 2.81265 triphosphate diphosphohydrolase 5 // 14q24 NM_005358 // LMO7 // UM domain 7 // LMO7 NM_005358 0.00460576 2.80795 13q22.2 // 4008 /// NM_015842 // LMO7 // LI NM_018667 // SMPD3 // sphingomyelin SMPD3 NM_018667 0.00228114 2.80665 phosphodiesterase 3, neutral membrane (neutr NM_004563 // PCK2 // phosphoenolpyruvate PCK2 NM_004563 0.00983672 2.79262 carboxykinase 2 (mitochondrial) // 14q1 NM_003657 // BCAS1 // breast carcinoma BCAS1 NM_003657 0.0213345 2.78368 amplified sequence 1 // 20q13.2 // 8537/ NM_024850 // BTNL8 // butyrophilin-like 8 // BTNL8 NM_024850 0.0446038 2.7769 5q35.3 // 79908 /// NM_001040462 // NM_020672 // S100A14 // S100 calcium S100A14 NM_020672 0.0202797 2.77156 binding protein A14 // 1q21.3 // 57402 /// NM_033229 // TRIM 15 // tripartite motif- TRIM15 NM_033229 0.0097609 2.77095 containing 15 // 6p21.3 // 89870 /// ENS NM_033229 // TRIM 15 // tripartite motif- TRIM15 NM_033229 0.0097609 2.77095 containing 15 // 6p21.3 // 89870 /// ENS NM_033229 // TRIM 15 // tripartite motif- TRIM15 NM_033229 0.0097609 2.77095 containing 15 // 6p21.3 // 89870 /// ENS NM_001144060 // NHSL1 // NHS-like 1 // NHSL1 NM_001144060 0.0124428 2.7705 6q23.3 // 57224 /// NM_020464 // NHSL1 // NM_003869 // CES2 // carboxylesterase 2 // CES2 NM_003869 0.0197746 2.76326 16q22.1 // 8824 /// NR_036684 // CES2 NM_199187 // KRT18 // keratin 18 // 12q13 // KRT18 NM_199187 0.0272938 2.7567 3875 /// NM_000224 // KRT18 // kera NM_002842 // PTPRH // protein tyrosine PTPRH NM_002842 0.00126103 2.75623 phosphatase, receptor type, H // 19q13.4 NM_001105248 // TMC5 // transmembrane TMC5 NM_001105248 0.015439 2.74553 channel-like 5 // 16p12.3 // 79838 /// NM_(—) NM_001145809 // MYH14 // myosin, heavy MYH14 NM_001145809 0.00203315 2.74198 chain 14, non-muscle // 19q13.33 // 79784 NM_001054 // SULT1A2 // sulfotransferase SULT1A2 NM_001054 0.0273843 2.73 family, cytosolic, 1A, phenol-preferrin NM_024850 // BTNL8 // butyrophilin-like 8 // BTNL8 NM_024850 0.0433332 2.7165 5q35.3 // 79908 /// NM_001159708 // NM_006147 // IRF6 // interferon regulatory IRF6 NM_006147 0.00663477 2.71435 factor 6 // 1q32.3-q41 // 3664 /// EN NM_000457 // HNF4A // hepatocyte nuclear HNF4A NM_000457 0.00414138 2.70616 factor 4, alpha // 20q13.12 // 3172 /// NM_138809 // CMBL // CMBL NM_138809 0.0336993 2.69623 carboxymethylenebutenolidase homolog (Pseudomonas) // 5p15. NM_001080467 // MYO5B // myosin VB // MYO5B NM_001080467 0.00639465 2.69568 18q21 // 4645 /// ENST00000285039 // MYO5B NM_153274 // BEST4 // bestrophin 4 // BEST4 NM_153274 0.0313639 2.68747 1p33-p32.3 // 266675 /// ENST00000372207/ NM_020775 // KIAA1324 // KIAA1324 // KIAA1324 NM_020775 0.0214297 2.68133 1p13.3 // 57535 /// ENST00000234923 // KIAA NM_001004320 // TMEM195 // transmembrane TMEM195 NM_001004320 0.0149666 2.67293 protein 195 // 7p21.2 // 392636 /// ENS NM_001091 // ABP1 // amiloride binding ABP1 NM_001091 0.0487109 2.66772 protein 1 (amine oxidase (copper-containi NM_016245 // HSD17B11 // hydroxysteroid HSD17B11 NM_016245 0.0216559 2.66473 (17-beta) dehydrogenase 11 // 4q22.1 // NM_006144 // GZMA // granzyme A GZMA NM_006144 0.00618242 2.66284 (granzyme 1, cytotoxic T-lymphocyte- associated s NM_001039372 // HEPACAM2 // HEPACAM family HEPACAM2 NM_001039372 0.0201907 2.6524 member 2 // 7q21.3 // 253012 /// NM_1 NM_001197097 // PRSS3 // protease, PRSS3 NM_001197097 0.0173103 2.63924 serine, 3 // 9p11.2 // 5646 /// NM_007343 // NM_012214 // MGAT4A // mannosyl (alpha- MGAT4A NM_012214 0.00113208 2.62742 1,3-)-glycoprotein beta-1,4-N-acetylgluco NM_019894 // TMPRSS4 // transmembrane TMPRSS4 NM_019894 0.0362683 2.60764 protease, serine 4 // 11q23.3 // 56649 /// NM_003810 // TNFSF10 // tumor necrosis TNFSF10 NM_003810 0.0129809 2.60509 factor (ligand) superfamily, member 10 // NM_022842 // CDCP1 // CUB domain CDCP1 NM_022842 0.0167874 2.60268 containing protein 1 // 3p21.31 // 64866 /// NM_(—) NM_001136493 // MFSD2A // major MFSD2A NM_001136493 0.00343618 2.59815 facilitator superfamily domain containing 2A // NM_018265 // C1orf 106 // chromosome 1 C1orf106 NM_018265 0.00613223 2.59677 open reading frame 106 // 1q32.1 // 55765 NM_000063 // C2 // complement component C2 NM_000063 0.0117239 2.59406 2 // 6p21.3 // 717 /// NM_001145903 // C NM_000063 // C2 // complement component C2 NM_000063 0.0117239 2.59406 2 // 6p21.3 // 717 /// NM_001145903 // C NM_000625 // NOS2 // nitric oxide synthase NOS2 NM_000625 0.0089305 2.59304 2, inducible // 17q11.2-q12 // 4843/ NM_001677 // ATP1B1 // ATPase, Na+/K+ ATP1B1 NM_001677 0.0131783 2.58871 transporting, beta 1 polypeptide // 1q24/ NM_004751 // GCNT3 // glucosaminyl (N- GCNT3 NM_004751 0.0432197 2.58761 acetyl) transferase 3, mucin type // 15q21 NM_002021 // FM01 // flavin containing FMO1 NM_002021 0.0408097 2.57646 monooxygenase 1 // 1q24.3 // 2326 /// ENS NM_033292 // CASP1 // caspase 1, CASP1 NM_033292 0.00634065 2.57013 apoptosis-related cysteine peptidase (interleuk NM_147161 // ACOT11 // acyl-CoA ACOT11 NM_147161 0.0462671 2.53682 thioesterase 11 // 1p32.3 // 26027 /// ENST00000 NM_001039112 // FER1L6 // fer-1-like 6 (C. FER1L6 NM_001039112 0.0413201 2.53444 elegans) // 8q24.1 // 654463 /// ENST NM_212543 // B4GALT4 // UDP- B4GALT4 NM_212543 0.00083206 2.53146 Gal:betaGIcNAc beta 1,4- galactosyltransferase, poly NM_182762 // MACC1 // metastasis MACC1 NM_182762 0.0113734 2.52994 associated in colon cancer 1 // 7p21.1 // 34638 NM_001461 // FMO5 // flavin containing FMO5 NM_001461 0.0227505 2.52925 monooxygenase 5 // 1q21.1 // 2330 /// NM NM_031219 // HDHD3 // haloacid HDHD3 NM_031219 0.00048055 2.52696 dehalogenase-like hydrolase domain containing 3/ NM_001010872 // FAM83B // family with FAM83B NM_001010872 0.00806204 2.52496 sequence similarity 83, member B // 6p12.1 NM_024533 // CHST5 // carbohydrate (N- CHST5 NM_024533 0.026327 2.51739 acetylglucosamine 6-O) sulfotransferase 5 NM_000063 // C2 // complement component C2 NM_000063 0.0114041 2.51419 2 // 6p21.3 // 717 /// NM_001145903 // C NM_004624 // VIPR1 // vasoactive intestinal VIPR1 NM_004624 0.00331244 2.50863 peptide receptor 1 // 3p22 // 7433 / NM_004572 // PKP2 // plakophilin 2 // 12p11 // PKP2 NM_004572 0.042448 2.49612 5318 /// NM_001005242 // PKP2 // NM_032521 // PARD6B // par-6 partitioning PARD6B NM_032521 0.00395798 2.49598 defective 6 homolog beta (C. elegans) NM_024915 // GRHL2 // grainyhead-like 2 GRHL2 NM_024915 0.00624177 2.49455 (Drosophila) // 8q22.3 // 79977 /// ENST NM_003982 // SLC7A7 // solute carrier SLC7A7 NM_003982 0.00813405 2.49274 family 7 (cationic amino acid transporter, NM_198584 // CA13 // carbonic anhydrase CA13 NM_198584 0.00510852 2.48988 XIII // 8q21.2 // 377677 /// ENST0000032 ENST00000319509 // MUC3A // mucin 3A, MUC3A ENST00000319509 0.0135883 2.4817 cell surface associated // 7q22 // 4584 // NM_021102 // SPINT2 // serine peptidase SPINT2 NM_021102 0.0219176 2.48131 inhibitor, Kunitz type, 2 // 19q13.1 // NM_080489 // SDCBP2 // syndecan binding SDCBP2 NM_080489 0.000789754 2.47862 protein (syntenin) 2 // 20p13 // 27111/ NM_001144967 // NEDD4L // neural NEDD4L NM_001144967 0.0227827 2.47791 precursor cell expressed, developmentally down- NM_001982 // ERBB3 // v-erb-b2 ERBB3 NM_001982 0.0175723 2.47531 erythroblastic leukemia viral oncogene homolog 3 NM_000240 // MAOA // monoamine oxidase MAOA NM_000240 0.0446884 2.47082 A // Xp11.3 // 4128 /// ENST00000338702/ NM_182960 // PRELID2 // PRELI domain PRELID2 NM_182960 0.00837834 2.47032 containing 2 // 5q32 // 153768 /// NM_13849 NM_017720 // STAP2 // signal transducing STAP2 NM_017720 0.016285 2.46781 adaptor family member 2 // 19p13.3 // 5 NM_138700 // TRIM40 // tripartite motif- TRIM40 NM_138700 0.0336507 2.45989 containing 40 // 6p22.1 // 135644 /// EN NM_000050 // ASS1 // argininosuccinate ASS1 NM_000050 0.0132614 2.43678 synthase 1 // 9q34.1 // 445 /// NM_054012 NM_005021 // ENPP3 // ectonucleotide ENPP3 NM_005021 0.0149678 2.43651 pyrophosphatase/phosphodiesterase 3 // 6q22 NM_001130080 // IFI27 // interferon, alpha- IFI27 NM_001130080 0.0140236 2.43613 inducible protein 27 // 14q32 // 3429 NM_001979 // EPHX2 // epoxide hydrolase EPHX2 NM_001979 0.00690804 2.43531 2, cytoplasmic // 8p21 // 2053 /// BC011 NM_017700 // ARHGEF38 // Rho guanine ARHGEF38 NM_017700 0.00476968 2.42966 nucleotide exchange factor (GEF) 38 // 4q24 NM_019080 // NDFIP2 // Nedd4 family NDFIP2 NM_019080 0.00576011 2.42832 interacting protein 2 // 13q31.1 // 54602 // NM_001135181 // SLC5A9 // solute carrier SLC5A9 NM_001135181 0.0296431 2.42215 family 5 (sodium/glucose cotransporter) NM_032717 // AGPAT9 // 1 -acylglycerol-3- AGPAT9 NM_032717 0.0147877 2.41843 phosphate O-acyltransferase 9 // 4q21.23 NM_001145303 // TMC4 // transmembrane TMC4 NM_001145303 0.00110774 2.41442 channel-like 4 // 19q13.42 // 147798 /// N NM_138700 // TRIM40 // tripartite motif- TRIM40 NM_138700 0.0250665 2.41358 containing 40 // 6p22.1 // 135644 /// EN NM_138700 // TRIM40 // tripartite motif- TRIM40 NM_138700 0.0250665 2.41358 containing 40 // 6p22.1 // 135644 /// EN NM_203463 // LASS6 // LAG1 homolog, LASS6 NM_203463 0.00156196 2.41203 ceramide synthase 6 // 2q24.3 // 253782 /// NM_001730 // KLF5 // Kruppel-like factor 5 KLF5 NM_001730 0.0129015 2.40278 (intestinal) // 13q22.1 // 688 /// EN NM_001265 // CDX2 // caudal type CDX2 NM_001265 0.0471437 2.402 homeobox 2 // 13q12.3 // 1045 /// ENST000003810 NM_000239 // LYZ // lysozyme // 12q15 // LYZ NM_000239 0.0118582 2.39899 4069 /// ENST00000261267 // LYZ // lyso NM_022772 // EPS8L2 // EPS8-like 2 // EPS8L2 NM_022772 0.00191717 2.39231 11p15.5 // 64787 /// ENST00000318562 // EP NM_025153 // ATP10B // ATPase, class V, ATP10B NM_025153 0.0273664 2.38677 type 10B // 5q34 // 23120 /// ENST000003 NM_178445 // CCRL1 // chemokine (C-C CCRL1 NM_178445 0.0328488 2.38032 motif) receptor-like 1 // 3q22 // 51554 /// NM_001031803 // LLGL2 // lethal giant LLGL2 NM_001031803 0.00351395 2.36948 larvae homolog 2 (Drosophila) // 17q25.1/ NM_175058 // PLEKHA7 // pleckstrin PLEKHA7 NM_175058 0.00170237 2.36502 homology domain containing, family A member 7 NM_006714 // SMPDL3A // sphingomyelin SMPDL3A NM_006714 0.0236138 2.36218 phosphodiesterase, acid-like 3A // 6q22.31 NR_024158 // LOC25845 // hypothetical LOC25845 NR_024158 0.0297858 2.35341 LOC25845 // 5p15.33 // 25845 /// ENST00000 NM_016339 // RAPGEFL1 // Rap guanine RAPGEFL1 NM_016339 0.026897 2.3526 nucleotide exchange factor (GEF)-like 1 // NM_015888 // HOOK1 // hook homolog 1 HOOK1 NM_015888 0.0336071 2.34842 (Drosophila) // 1p32.1 // 51361 /// ENST000 NM_138737 // HEPH // hephaestin // Xq11- HEPH NM_138737 0.0118198 2.34595 q12 // 9843 /// NM_001130860 // HEPH // NM_012079 // DGAT1 // diacylglycerol O- DGAT1 NM_012079 0.023252 2.34522 acyltransferase 1 // 8q24.3 // 8694 /// E NM_012079 // DGAT1 // diacylglycerol O- DGAT1 NM_012079 0.023252 2.34522 acyltransferase 1 // 8q24.3 // 8694 /// E NM_001017535 // VDR // vitamin D (1,25- VDR NM_001017535 0.0115491 2.34153 dihydroxyvitamin D3) receptor // 12q13.1 NM_001029874 // REP15 // RAB15 effector REP15 NM_001029874 0.0477963 2.33656 protein // 12p11.22 // 387849 /// ENST00 NM_198495 // CTAGE4 // CTAGE family, CTAGE4 NM_198495 0.00065154 2.33596 member 4 // 7q35 // 100128553 /// NM_001145 NM_006548 // IGF2BP2 // insulin-like growth IGF2BP2 NM_006548 8.80E−05 2.33476 factor 2 mRNA binding protein 2 // 3 NM_002985 // CCL5 // chemokine (C-C CCL5 NM_002985 0.0247261 2.33002 motif) ligand 5 // 17q11,2-q12 // 6352 /// E NM_001005328 // OR2A7 // olfactory OR2A7 NM_001005328 0.00337105 2.32021 receptor, family 2, subfamily A, member 7 // NM_018284 // GBP3 // guanylate binding GBP3 NM_018284 0.013933 2.31798 protein 3 // 1p22.2 // 2635 /// ENST00000 NM_002829 // PTPN3 // protein tyrosine PTPN3 NM_002829 0.0212048 2.31511 phosphatase, non-receptor type 3 // 9q31 NM_021073 // BMP5 // bone morphogenetic BMP5 NM_021073 0.0201876 2.31001 protein 5 // 6p12.1 // 653 /// ENST00000 NM_178176 // MOGAT3 // monoacylglycerol MOGAT3 NM_178176 0.00641018 2.30988 O-acyltransferase 3 // 7q22.1 // 346606 NM_000666 // ACY1 // aminoacylase 1 // ACY1 NM_000666 0.0261486 2.30581 3p21.1 // 95 /// L07548 // ACY1 // aminoa NM_001098634 // RBM47 // RNA binding RBM47 NM_001098634 0.00857247 2.30203 motif protein 47 // 4p14 // 54502 /// NM_01 NM_080658 // ACY3 // aspartoacylase ACY3 NM_080658 0.0498753 2.301 (aminocyclase) 3 // 11q13.2 // 91703 /// ENS NR_003587 // MYO15B // myosin XVB MYO15B NR_003587 0.00759021 2.29754 pseudogene // 17q25.1 // 80022 /// BC027875 // NM_005435 // ARHGEF5 // Rho guanine ARHGEF5 NM_005435 0.00766916 2.29684 nucleotide exchange factor (GEF) 5 // 7q33-q NM_005435 // ARHGEF5 // Rho guanine ARHGEF5 NM_005435 0.00846455 2.29311 nucleotide exchange factor (GEF) 5 // 7q33-q NM_001017967 // MARVELD3 // MARVEL MARVELD3 NM_001017967 0.0124186 2.2921 domain containing 3 // 16q22.2 // 91862 /// N NM_003389 // CORO2A // coronin, actin CORO2A NM_003389 0.0203606 2.28709 binding protein, 2A // 9q22.3 // 7464 /// NM_031469 // SH3BGRL2 // SH3 domain SH3BGRL2 NM_031469 0.0214373 2.27245 binding glutamic acid-rich protein like 2 // NM_030766 // BCL2L14 // BCL2-like 14 BCL2L14 NM_030766 0.0037691 2.26634 (apoptosis facilitator) // 12p13-p12 // 793 NR_002713 // NPY6R // neuropeptide Y NPY6R NR_002713 0.0429642 2.26407 receptor Y6 (pseudogene) // 5q31 // 4888 // NM_001114086 // CLIC5 // chloride CLIC5 NM_001114086 0.0269601 2.25433 intracellular channel 5 // 6p12.3 // 53405 /// NM_003645 // SLC27A2 // solute carrier SLC27A2 NM_003645 0.040906 2.2539 family 27 (fatty acid transporter), membe NM_001136050 // DHRS1 // DHRS1 NM_001136050 0.000608529 2.23931 dehydrogenase/reductase (SDR family) member 1 // 14q12 NM_002164 // IDO1 // indoleamine 2,3- IDO1 NM_002164 0.00532092 2.2314 dioxygenase 1 // 8p12-p11 // 3620 /// ENSTO NM_001171192 // GDPD2 // GDPD2 NM_001171192 0.0455387 2.23073 glycerophosphodiester phosphodiesterase domain containi NM_016445 // PLEK2 // pleckstrin 2 // PLEK2 NM_016445 0.0184048 2.22972 14q23.3 // 26499 /// ENST00000216446 // PL NR_033122 // PDZD3 // PDZ domain PDZD3 NR_033122 0.0104609 2.2269 containing 3 // 11q23.3 // 79849 /// NM_0011684 NM_000932 // PLCB3 // phospholipase C, PLCB3 NM_000932 0.01393 2.22018 beta 3 (phosphatidylinositol-specific) // NM_018235 // CNDP2 // CNDP dipeptidase CNDP2 NM_018235 0.000958173 2.20566 2 (metallopeptidase M20 family) // 18q22. NM_032562 // PLA2G12B // phospholipase PLA2G12B NM_032562 0.0420214 2.20423 A2, group XIIB // 10q22.1 // 84647 /// EN NM_021080 // DAB1 // disabled homolog 1 DAB1 NM_021080 0.04076 2.20106 (Drosophila) // 1p32-p31 // 1600 /// ENS NM_001710 // CFB // complement factor B // CFB NM_001710 0.00181667 2.19954 6p21.3 // 629 /// ENST00000425368 // NM_183240 // TM EM37 // transmembrane TMEM37 NM_183240 0.0487149 2.19842 protein 37 // 2q14.2 // 140738 /// ENST0000 AK127847 // FLJ45950 // FLJ45950 protein // FLJ45950 AK127847 0.00195329 2.198 11q24.3 // 399975 NM_001710 // CFB // complement factor B // CFB NM_001710 0.00220919 2.19758 6p21.3 // 629 III ENST00000417261 // NM_144590 // ANKRD22 // ankyrin repeat ANKRD22 NM_144590 0.0445105 2.19752 domain 22 // 10q23.31 // 118932 /// ENSTO NM_002067 // GNA11 // guanine nucleotide GNA11 NM_002067 0.014093 2.19185 binding protein (G protein), alpha 11 ( NM_006579 // EBP // emopamil binding EBP NM_006579 0.0115147 2.18786 protein (sterol isomerase) // Xp11.23-p11.2 NM_014873 // LPGAT1 // LPGAT1 NM_014873 0.000550666 2.18469 lysophosphatidylglycerol acyltransferase 1 // 1q32 // 992 NM_030943 // AMN // amnionless homolog AMN NM_030943 0.00168811 2.18289 (mouse) // 14q32.3 // 81693 /// ENST00000 NM_016548 // GOLM1 // golgi membrane GOLM1 NM_016548 0.0424472 2.18243 protein 1 // 9q21.33 // 51280 /// NM_177937 NM_032148 // SLC41A2 // solute carrier SLC41A2 NM_032148 0.0301277 2.17752 family 41, member 2 // 12q23.3 // 84102/ NM_000949 // PRLR // prolactin receptor // PRLR NM_000949 0.0313649 2.17608 5p13.2 // 5618 /// ENST00000382002 // NM_181642 // SPINT1 // serine peptidase SPINT1 NM_181642 0.0361797 2.17498 inhibitor, Kunitz type 1 // 15q15.1 // 6 NM_001113567 // C17orf76 // chromosome C17orf76 NM_001113567 0.0248369 2.17219 17 open reading frame 76 // 17p11.2 // 38 NM_000355 // TCN2 // transcobalamin II // TCN2 NM_000355 0.0233279 2.17134 22q12.2 // 6948 /// NM_001184726 // TC NM_015198 // COBL // cordon-bleu COBL NM_015198 0.0208672 2.1656 homolog (mouse) // 7p12.1 // 23242 /// ENST0000 NM_024616 // C3orf52 // chromosome 3 C3orf52 NM_024616 0.00881101 2.16302 open reading frame 52 // 3q13.2 // 79669 // NM_020469 // ABO // ABO blood group ABO NM_020469 0.00222828 2.16292 (transferase A, alpha 1-3-N-acetylgalactosam NM_030908 // OR2A4 // olfactory receptor, OR2A4 NM_030908 0.00568966 2.15894 family 2, subfamily A, member 4 // 6q2 NM_003980 // MAP7 // microtubule- MAP7 NM_003980 0.0037529 2.15742 associated protein 7 // 6q23.3 // 9053 /// NM_0 NM_017417 // GALNT8 // UDP-N-acetyl- GALNT8 NM_017417 0.013696 2.15417 alpha-D-galactosamine: polypeptide N-acetylga NM_005410 // SEPP1 // selenoprotein P, SEPP1 NM_005410 0.0133071 2.15347 plasma, 1 // 5q31 // 6414 /// NM_00108548 NM_152573 // RASEF // RAS and EF-hand RASEF NM_152573 0.0366785 2.15133 domain containing // 9q21.32 // 158158 /// NM_006633 // IQGAP2 // IQ motif containing IQGAP2 NM_006633 0.00969849 2.1509 GTPase activating protein 2 // 5q13.3 NM_152550 // SH3RF2 // SH3 domain SH3RF2 NM_152550 0.00614396 2.15072 containing ring finger 2 // 5q32 // 153769 /// NM_018686 // CMAS // cytidine CMAS NM_018686 0.0124234 2.14998 monophosphate N-acetylneuraminic acid synthetase/ NM_025045 // BAIAP2L2 // BA11-associated BAIAP2L2 NM_025045 0.0129162 2.14195 protein 2-like 2 // 22q13.1 // 80115 // NM_001859 // SLC31A1 // solute carrier SLC31A1 NM_001859 0.00838827 2.13821 family 31 (copper transporters), member 1 NM_016614 // TDP2 // tyrosyl-DNA TDP2 NM_016614 0.0246156 2.13573 phosphodiesterase 2 // 6p22.3-p22.1 // 51567 // NM_003848 // SUCLG2 // succinate-CoA SUCLG2 NM_003848 0.00569037 2.13077 ligase, GDP-forming, beta subunit // 3p14.1 NM_017904 // TTC22 // tetratricopeptide TTC22 NM_017904 0.0153126 2.12827 repeat domain 22 // 1p32.3 // 55001 /// NM_003060 // SLC22A5 // solute carrier SLC22A5 NM_003060 0.02024 2.12394 family 22 (organic cation/carnitine trans NM_002662 // PLD1 // phospholipase D1, PLD1 NM_002662 0.0135876 2.12113 phosphatidylcholine-specific // 3q26 // 5 NM_018964 // SLC37A1 // solute carrier SLC37A1 NM_018964 0.0229039 2.12062 family 37 (glycerol-3-phosphate transport NM_001251 // CD68 // CD68molecule // CD68 NM_001251 0.00105743 2.11575 17p13 // 968 /// NM_001040059 // CD68 // C NM_174941 // CD163L1 // CD163 molecule- CD163L1 NM_174941 0.00407203 2.11396 like 1 // 12p13.3 // 283316 /// ENST00000 NM_016029 // DHRS7 // DHRS7 NM_016029 0.0124063 2.11159 dehydrogenase/reductase (SDR family) member 7 // 14q23.1/ NM_024101 // MLPH // melanophilin // MLPH NM_024101 0.00197625 2.10533 2q37.3 // 79083 /// NM_001042467 // MLPH // NM_004670 // PAPSS2 // 3′- PAPSS2 NM_004670 0.0403309 2.10272 phosphoadenosine 5′-phosphosulfate synthase 2 // 10q24 AK172782 // GPAM // glycerol-3-phosphate GPAM AK172782 0.0314353 2.09633 acyltransferase, mitochondrial // 10q25 NM_001142685 // ARHGAP32 // Rho ARHGAP32 NM_001142685 0.00415504 2.09203 GTPase activating protein 32 // 11q24.3 // 9743 NM_198495 // CTAGE4 // CTAGE family, CTAGE4 NM_198495 0.00141321 2.0906 member 4 // 7q35 // 100128553 /// NM_001145 ENST00000439698 // P4HA2 // prolyl 4- P4HA2 ENST00000439698 0.0142839 2.08741 hydroxylase, alpha polypeptide II // 5q31/ NM_015020 // PHLPP2 // PH domain and PHLPP2 NM_015020 0.013905 2.08634 leucine rich repeat protein phosphatase 2/ NM_004252 // SLC9A3R1 // solute carrier SLC9A3R1 NM_004252 0.00776993 2.0857 family 9 (sodium/hydrogen exchanger), me NM_012243 // SLC35A3 // solute carrier SLC35A3 NM_012243 0.0307101 2.07986 family 35 (UDP-N-acetylglucosamine (UDP-G NM_020184 // CNNM4 // cyclin M4 // 2q11 // CNNM4 NM_020184 0.02685 2.07897 26504 /// ENST00000377075 // CNNM4 // NM_001490 // GCNT1 // glucosaminyl (N- GCNT1 NM_001490 0.00172819 2.07671 acetyl) transferase 1, core 2 // 9q13 // 2 NM_003667 // LGR5 // leucine-rich repeat- LGR5 NM_003667 0.0237574 2.07254 containing G protein-coupled receptor 5 NM_001966 // EHHADH // enoyl-CoA, EHHADH NM_001966 0.0130422 2.07114 hydratase/3-hydroxyacyl CoA dehydrogenase // 3 NM_017726 // PPP1R14D // protein PPP1R14D NM_017726 0.0497008 2.07017 phosphatase 1, regulatory (inhibitor) subunit 1 NM_006994 // BTN3A3 // butyrophilin, BTN3A3 NM_006994 0.00121808 2.06925 subfamily 3, member A3 // 6p21.3 // 10384/ NM_001039724 // NOSTRIN // nitric oxide NOSTRIN NM_001039724 0.00986343 2.06731 synthase trafficker // 2q31.1 // 115677 NR_026912 // ABHD11 // abhydrolase ABHD11 NR_026912 0.000593971 2.05896 domain containing 11 // 7q11.23 // 83451 /// NM_001145206 // KIAA1671 // KIAA1671 // KIAA1671 NM_001145206 0.00446756 2.05612 22q11.23 // 85379 /// ENST00000358431 // NM_153345 // TM EM 139 // transmembrane TMEM139 NM_153345 0.00505302 2.05293 protein 139 // 7q34 // 135932 /// ENST0000 NM_001164694 // IYD // iodotyrosine IYD NM_001164694 0.022189 2.05208 deiodinase // 6q25.1 // 389434 /// NM_203395 NM_016472 // C14orf 129 // chromosome 14 C14orf129 NM_016472 0.048055 2.04519 open reading frame 129 // 14q32.2 // 515 NM_001017402 // LAMB3 // laminin, beta 3 // LAMB3 NM_001017402 0.0267716 2.04174 1q32 // 3914 III NM_001127641 // LAM NM_004999 // MYO6 // myosin VI // 6q13 // MYO6 NM_004999 0.00369349 2.04095 4646 /// ENST00000369977 // MYO6 // my NR_027244 // LOC151009 // hypothetical LOC151009 NR_027244 0.0115721 2.04078 LOC151009 // 2q13 // 151009 /// NR_027244 AB065085 // TOM1L1 // target of myb1 TOM1L1 AB065085 0.04656 2.03713 (chicken)-like 1 // 17q23.2 // 10040 NM_017750 // RETSAT // retinol saturase RETSAT NM_017750 0.0184264 2.03345 (all-trans-retinol 13,14-reductase) // 2 NM_004721 // MAP3K13 // mitogen- MAP3K13 NM_004721 0.00937615 2.03148 activated protein kinase kinase kinase 13 // 3q2 NM_018677 // ACSS2 // acyl-CoA ACSS2 NM_018677 0.0306269 2.02661 synthetase short-chain family member 2 // 20q11.2 NM_014317 // PDSS1 // prenyl (decaprenyl) PDSS1 NM_014317 0.0365076 2.02171 diphosphate synthase, subunit 1 // 10p NM_014498 // GOLIM4 // golgi integral GOLIM4 NM_014498 0.00240934 2.02056 membrane protein 4 // 3q26.2 // 27333 /// NM_033429 // CALML4 // calmodulin-like 4 // CALML4 NM_033429 0.0419784 2.01981 15q23 // 91860 III NM_001031733 // C NR_036751 // HSP90AA6P // heat shock HSP90AA6P NR_036751 0.0220954 2.01604 protein 90 kDa alpha (cytosolic), class A me NM_012120 // CD2AP // CD2-associated CD2AP NM_012120 0.00502091 2.0122 protein // 6p12 // 23607 /// ENST0000035931 NM_005536 // IMPA1 // inositol(myo)-1 (or IMPA1 NM_005536 0.0194688 2.01203 4)-monophosphatase 1 // 8q21.13-q21.3/ NM_001153 // ANXA4 // annexinA4 // 2p13 // ANXA4 NM_001153 0.0255723 2.01151 307 /// ENST00000394295 // ANXA4 // NM_000147 // FUCA1 // fucosidase, alpha- FUCA1 NM_000147 0.00469253 2.0105 L-1, tissue // 1p34 // 2517 /// ENST000 NM_003774 // GALNT4 // UDP-N-acetyl- GALNT4 NM_003774 0.00622316 2.00871 alpha-D-galactosamine: polypeptide N- acetylga NM_001122890 // GGT6 // gamma- GGT6 NM_001122890 0.0328357 2.00627 glutamyltransferase 6 // 17p13.2 // 124975 /// NM_(—) NM_001164277 // SLC37A4 // solute carrier SLC37A4 NM_001164277 0.0068184 2.00477 family 37 (glucose-6-phosphate transpo NM_001565 // CXCL10 // chemokine (C-X-C CXCL10 NM_001565 0.0468134 2.00368 motif) ligand 10 // 4q21 // 3627 /// ENS NM_005030 // PLK1 // polo-like kinase 1 // PLK1 NM_005030 0.0109795 2.00251 16p12.2 // 5347 /// ENST00000300093/ NM_001012631 // IL32 // interleukin 32 // IL32 NM_001012631 0.0214868 2.00238 16p13.3 // 9235 /// NM_004221 // IL32 NM_005309 // GPT // glutamic-pyruvate GPT NM_005309 0.0098254 2.00201 transaminase (alanine aminotransferase) // NM_005159 // ACTC1 // actin, alpha, ACTC1 NM_005159 0.00451989 −2.00712 cardiac muscle 1 // 15q11 -q14 // 70 /// ENST NM_130385 // MRVI1 // murine retrovirus MRVI1 NM_130385 0.0186352 −2.00908 integration site 1 homolog // 11p15 // 1 NR_003329 // SNORD116-14 // small SNORD116-14 NR_003329 0.00710694 −2.01066 nucleolar RNA, C/D box 116-14 // 15q11.2 // 10 NM_030751 // ZEB1 // zinc finger E-box ZEB1 NM_030751 0.0190641 −2.01665 binding homeobox 1 // 10p11.2 // 6935 /// NM_001321 // CSRP2 // cysteine and CSRP2 NM_001321 0.0130189 −2.01975 glycine-rich protein 2 // 12q21.1 // 1466 /// NM_199460 // CACNA1C // calcium CACNA1C NM_199460 0.0164629 −2.03364 channel, voltage-dependent, L type, alpha 1C sub NM_007078 // LDB3 // LIM domain binding 3 // LDB3 NM_007078 0.013344 −2.03636 10q22.3-q23.2 // 11155 /// NM_00117 ENST00000436525 // C15orf51 // dynamin 1 C15orf51 ENST00000436525 0.0479813 −2.04311 pseudogene // 15q26.3 // 196968 ENST00000436525 // C15orf51 // dynamin 1 C15orf51 ENST00000436525 0.0479813 −2.04311 pseudogene // 15q26.3 // 196968 NM_001042454 // TGFB111 // transforming TGFB1I1 NM_001042454 0.0141045 −2.0503 growth factor beta 1 induced transcript NM_201266 // NRP2 // neuropilin 2 // 2q33.3 // NRP2 NM_201266 0.0231808 −2.05329 8828 /// NM_003872 // NRP2 // neu NM_014286 // NCS1 // neuronal calcium NCS1 NM_014286 0.0400809 −2.05571 sensori // 9q34 // 23413 /// NM_001128826 NR_002960 // SNORA20 // small nucleolar SNORA20 NR_002960 0.0102255 −2.05618 RNA, H/ACA box 20 // 6q25.3 // 677806 NR_023343 // RNU4ATAC // RNA, U4atac RNU4ATAC NR_023343 0.0114016 −2.05953 small nuclear (U12-dependent splicing) // 2 NM_003829 // MPDZ // multiple PDZ MPDZ NM_003829 0.0230169 −2.06542 domain protein // 9p23 // 8777 /// ENST0000038 NM_182734 // PLCB1 // phospholipase C, PLCB1 NM_182734 0.0285626 −2.0675 beta 1 (phosphoinositide-specific) // 20p NM_212482 // FN1 // fibronectin 1 // 2q34 // FN1 NM_212482 0.0289963 −2.06817 2335 /// NM_002026 // FN1 // fibron NM_001166292 // PTCH2 // patched 2 // PTCH2 NM_001166292 0.0155977 −2.06949 1p34.1 // 8643 /// ENST00000438067 // PTCH NM_001128310 // SPARCL1 // SPARC-like SPARCL1 NM_001128310 0.0275433 −2.0695 1 (hevin) // 4q22.1 // 8404 /// NM_004684 NR_003332 // SNORD116-17 // small SNORD116-17 NR_003332 0.00123218 −2.07085 nucleolar RNA, C/D box 116-17 // 15q11.2 // 10 NR_003332 // SNORD116-17 // small SNORD116-17 NR_003332 0.00123218 −2.07085 nucleolar RNA, C/D box 116-17 // 15q11.2 // 10 NM_001390 // DTNA // dystrobrevin, alpha // DTNA NM_001390 0.0140008 −2.07227 18q12 // 1837 /// NM_032975 // DTNA NM_172316 // MEIS2 // Meis homeobox 2 // MEIS2 NM_172316 0.012629 −2.07482 15q14 // 4212 /// NM_170677 // MEIS2 // NM_032801 // JAM3 // junctional adhesion JAM3 NM_032801 0.00375191 −2.08055 molecule 3 // 11q25 // 83700 /// ENST00 NM_001496 // GFRA3 // GDNF family GFRA3 NM_001496 0.0143176 −2.08436 receptor alpha 3 // 5q31.1-q31.3 // 2676 /// E NM_003116 // SPAG4 // sperm associated SPAG4 NM_003116 0.0370178 −2.09743 antigen 4 // 20q11.21 // 6676 /// ENST000 NR_002754 // RNU5E // RNA, U5E small RNU5E NR_002754 0.0153145 −2.10499 nuclear // 1p36.22 // 26829 /// M77839 // R NM_000109 // DM D // dystrophin // Xp21.2 // DMD NM_000109 0.0305823 −2.10535 1756 /// NM_004010 // DMD // dystrop NM_005725 // TSPAN2 // tetraspanin 2 // TSPAN2 NM_005725 0.00484522 −2.10726 1p13.2 // 10100 /// ENST00000369516 // T ENST00000436525 // C15orf51 // dynamin 1 C15orf51 ENST00000436525 0.0401346 −2.11861 pseudogene // 15q26.3 // 196968 NM_001190839 // MGP // matrix Gia protein // MGP NM_001190839 0.0229696 −2.13146 12p12.3 // 4256 /// NM_000900 // MG NM_031442 // TMEM47 // transmembrane TMEM47 NM_031442 0.0162367 −2.16059 protein 47 // Xp11.4 // 83604 /// ENST00000 NM_002776 // KLK10 // kallikrein-related KLK10 NM_002776 0.0131782 −2.16442 peptidase 10 // 19q13 // 5655 /// NM_14 NM_134269 // SMTN // smoothelin // SMTN NM_134269 0.0278447 −2.16615 22q12.2 // 6525 /// NM_134270 // SMTN // smoo NM_002742 // PRKD1 // protein kinase D1 // PRKD1 NM_002742 0.0208525 −2.17797 14q11 // 5587 /// ENST00000331968 // NM_001001396 // ATP2B4 // ATPase, Ca++ ATP2B4 NM_001001396 0.0372252 −2.18014 transporting, plasma membrane 4 // 1q32.1 NM_005451 // PDLIM7 // PDZ and LIM PDLIM7 NM_005451 0.00654348 −2.18595 domain 7 (enigma) // 5q35.3 // 9260 /// NM_20 NR_002952 // SNORA9 // small nucleolar SNORA9 NR_002952 0.0244704 −2.19918 RNA, H/ACA box 9 // 7p13 // 677798 /// AK NM_003069 // SMARCA1 // SWI/SNF SMARCA1 NM_003069 0.00571381 −2.2109 related, matrix associated, actin dependent regu NR_003330 // SNORD116-15 // small SNORD116-15 NR_003330 6.72E−05 −2.21218 nucleolar RNA, C/D box 116-15 // 15q11.2 // 10 NM_002398 // MEIS1 // Meis homeobox 1 // MEIS1 NM_002398 0.0208728 −2.21341 2p14 // 4211 /// ENST00000272369 // MEI ENST00000436525 // C15orf51 // dynamin 1 C15orf51 ENST00000436525 0.0297132 −2.22015 pseudogene // 15q26.3 // 196968 ENST00000436525 // C15orf51 // dynamin 1 C15orf51 ENST00000436525 0.0297132 −2.22015 pseudogene // 15q26.3 // 196968 NM_003734 // AOC3 // amine oxidase, AOC3 NM_003734 0.0151647 −2.22019 copper containing 3 (vascular adhesion prote AF391113 // C21orf70 // chromosome 21 C21orf70 AF391113 0.00109586 −2.22308 open reading frame 70 // 21q22.3 // 85395 NM_001937 // DPT // dermatopontin // 1q12- DPT NM_001937 0.0379186 −2.22359 q23 // 1805 /// ENST00000367817 // DPT NM_012232 // PTRF // polymerase I and PTRF NM_012232 0.0194925 −2.23107 transcript release factor // 17q21.2 // 28 NM_024605 // ARHGAP10 // Rho GTPase ARHGAP10 NM_024605 0.00832518 −2.23204 activating protein 10 // 4q31.23 // 79658 // NM_022117 // TSPYL2 // TSPY-like2 // TSPYL2 NM_022117 0.0134024 −2.23502 Xp11.2 // 64061 /// ENST00000375442 // TSP NM_005100 // AKAP12 // A kinase (PRKA) AKAP12 NM_005100 0.0357306 −2.24089 anchor protein 12 // 6q24-q25 // 9590 /// AY423733 // DDR2 // discoidin domain DDR2 AY423733 0.0358613 −2.2447 receptor tyrosine kinase 2 // 1q23.3 // 492 NM_153703 // PODN // podocan // 1p32.3 // PODN NM_153703 0.0277365 −2.26923 127435 /// ENST00000312553 // PODN // NM_004370 // COL12A1 // collagen, type COL12A1 NM_004370 0.0499701 −2.27002 XII, alpha 1 // 6q12-q13 // 1303 /// NM_0 NM_004137 // KCNMB1 // potassium large KCNMB1 NM_004137 0.0277682 −2.27584 conductance calcium-activated channel, su NM_014575 // SCHIP1 // schwannomin SCHIP1 NM_014575 0.00470657 −2.28272 interacting protein 1 // 3q25.32-q25.33 // 29 NM_001753 // CAV1 // caveolin 1,caveolae CAV1 NM_001753 0.0368534 −2.29054 protein, 22kDa // 7q31.1 // 857 /// NM NM_002338 // LSAMP // limbic system- LSAMP NM_002338 0.0456749 −2.30408 associated membrane protein // 3q13.2-q21 // NM_058229 // FBXO32 // F-box protein 32 // FBXO32 NM_058229 0.0422526 −2.30763 8q24.13 // 114907 /// NM_148177 // FB NM_006765 // TUSC3 // tumor suppressor TUSC3 NM_006765 0.00173576 −2.32217 candidate 3 // 8p22 // 7991 /// NM_178234 NM_015687 // FILIP1 // filamin A interacting FILIP1 NM_015687 0.0158717 −2.32321 protein 1 // 6q14.1 // 27145 /// EN NM_006080 // SEMA3A // sema domain, SEMA3A NM_006080 0.0142131 −2.32699 immunoglobulin domain (Ig), short basic doma NM_000922 // PDE3B // phosphodiesterase PDE3B NM_000922 0.00420057 −2.33135 3B, cGMP-inhibited // 11p15.1 // 5140 // NM_000722 // CACNA2D1 // calcium CACNA2D1 NM_000722 0.0107345 −2.33411 channel, voltage-dependent, alpha 2/delta subun NM_001197294 // DPYSL3 // dihydropyrimidinase- DPYSL3 NM_001197294 0.0231385 −2.33517 like 3 // 5q32 // 1809 /// NM_0013 NM_172311 // STON1-GTF2A1L // STON1- TON1-GTF2A1 NM_172311 0.0264382 −2.33729 GTF2A1L readthrough // 2p16.3 // 286749 /// NM_000857 // GUCY1B3 // guanylate GUCY1B3 NM_000857 0.0141507 −2.34285 cyclase 1, soluble, beta 3 // 4q31.3-q33 // 29 NR_033662 // CSF3 // colony stimulating CSF3 NR_033662 0.036854 −2.35397 factor 3 (granulocyte) // 17q11.2-q12 // NM_001706 // BCL6 // B-cell CLL/lymphoma BCL6 NM_001706 0.0395014 −2.37213 6 // 3q27 // 604 /// NM_001130845 // BC NM_014112 // TRPS1 // trichorhinophalangeal TRPS1 NM_014112 0.021813 −2.37338 syndrome I // 8q24.12 // 7227 /// EN NM_003275 // TMOD1 // tropomodulin 1 // TMOD1 NM_003275 0.00926909 −2.39163 9q22.3 // 7111 /// NM_001166116 // TMOD1 NM_004040 // RHOB // ras homolog gene RHOB NM_004040 0.00209611 −2.39166 family, member B // 2p24 // 388 /// ENST00 NM_007281 // SCRG1 // stimulator of SCRG1 NM_007281 0.0449505 −2.42771 chondrogenesis 1 // 4q34.1 // 11341 /// ENST NM_053025 // MYLK // myosin light chain MYLK NM_053025 0.0334323 −2.44896 kinase // 3q21 // 4638 /// NM_053026 // NM_133646 // ZAK // sterile alpha motif and ZAK NM_133646 0.0101002 −2.45225 leucine zipper containing kinase AZK NM_001123364 // C6orf 186 // chromosome C6orf186 NM_001123364 0.0338175 −2.45305 6 open reading frame 186 // 6q21 // 72846 NM_005909 // MAPI B // microtubule- MAP1B NM_005909 0.00199713 −2.45363 associated protein 1B // 5q13 // 4131 /// ENST NM_001136191 // KANK2 // KN motif and KANK2 NM_001136191 0.00418 −2.45823 ankyrin repeat domains 2 // 19p13.2 // 259 NR_002836 // PGM5P2 // phosphoglucomutase PGM5P2 NR_002836 0.0106051 −2.46207 5 pseudogene 2 // 9q12 // 595135 /// N NM_006988 // ADAMTS1 // ADAM ADAMTS1 NM_006988 0.0212926 −2.47602 metallopeptidase with thrombospondin type 1 motif, NM_001897 // CSPG4 // chondroitin sulfate CSPG4 NM_001897 0.000233664 −2.47738 proteoglycan 4 // 15q24.2 // 1464 /// NM_012134 // LMOD1 // leiomodin 1 LMOD1 NM_012134 0.0254164 −2.48821 (smooth muscle) // 1q32 // 25802 /// ENST00000 NM_000856 // GUCY1A3 // guanylate GUCY1A3 NM_000856 0.0154068 −2.49669 cyclase 1, soluble, alpha 3 // 4q31.3-q33|4q31 NR_002196 // H19 // H19, imprinted H19 NR_002196 0.0422207 −2.49895 maternally expressed transcript (non-protein NM_002667 // PLN // phospholamban // PLN NM_002667 0.0458219 −2.50528 6q22.1 // 5350 /// ENST00000357525 // PLN/ NM_004078 // CSRP1 // cysteine and CSRP1 NM_004078 0.0389579 −2.51599 glycine-rich protein 1 // 1q32 // 1465 /// NM NM_001141945 // ACTA2 // actin, alpha2, ACTA2 NM_001141945 0.00367966 −2.51621 smooth muscle, aorta // 10q23.3 // 59/ NM_002986 // CCL11 // chemokine(C-C CCL11 NM_002986 0.0132628 −2.5178 motif) ligand 11 // 17q21.1-q21.2 // 6356/ NM_033138 // CALD1 // caldesmon 1 // CALD1 NM_033138 0.0229067 −2.51869 7q33 // 800 /// NM_033157 // CALD1 // calde NM_001164836 // FXYD6 // FXYD domain FXYD6 NM_001164836 0.0202065 −2.53004 containing ion transport regulator 6 // 11q NM_003725 // HSD17B6 // hydroxysteroid HSD17B6 NM_003725 0.0196889 −2.54527 (17-beta) dehydrogenase 6 homolog (mouse) NM_001146312 // MYOCD // myocardin // MYOCD NM_001146312 0.0298805 −2.59465 17p11.2 // 93649 /// NM_153604 // MYOCD // NM_015225 // PRUNE2 // prune homolog 2 PRUNE2 NM_015225 0.0217217 −2.59492 (Drosophila) // 9q21.2 // 158471 /// AB53 NM_001168278 // WWTR1 // WW domain WWTR1 NM_001168278 0.014475 −2.60243 containing transcription regulator 1 // 3q23- NM_001008711 // RBPMS // RNA binding RBPMS NM_001008711 0.00600769 −2.60406 protein with multiple splicing // 8p12 // 1 NM_001014796 // DDR2 // discoidin domain DDR2 NM_001014796 0.00523497 −2.61121 receptor tyrosine kinase 2 // 1q23.3 // NM_018640 // LMO3 // UM domain only 3 LMO3 NM_018640 0.042971 −2.63105 (rhombotin-like 2) // 12p12.3 // 55885 // NR_002836 // PGM5P2 // phosphoglucomutase PGM5P2 NR_002836 0.00678244 −2.64929 5 pseudogene 2 // 9q12 // 595135 /// N NM_021914 // CFL2 // cofilin 2 (muscle) // CFL2 NM_021914 0.0261349 −2.65343 14q12 // 1073 /// NM_138638 // CFL2/ NM_016277 // RAB23 // RAB23, member RAB23 NM_016277 0.035448 −2.66122 RAS oncogene family // 6p11 // 51715 /// NM_(—) NM_145234 // CHRDL1 // chordin-like 1 // CHRDL1 NM_145234 0.00265317 −2.67563 Xq23 // 91851 /// NM_001143981 // CHRDL NM_001134439 // PHLDB2 // pleckstrin PHLDB2 NM_001134439 0.0258326 −2.67775 homology-like domain, family B, member 2 // NM_006832 // FERMT2 // fermitin family FERMT2 NM_006832 0.0205617 −2.7145 member 2 // 14q22.1 // 10979 /// NM_00113 NM_001128205 // SULF1 // sulfatase 1 // SULF1 NM_001128205 0.0335496 −2.73234 8q13.1 // 23213 /// NM_015170 // SULF1/ NM_194272 // RBPMS2 // RNA binding RBPMS2 NM_194272 0.012053 −2.74286 protein with multiple splicing 2 // 15q22.31 NM_014476 // PDLIM3 // PDZ and LIM PDLIM3 NM_014476 0.0110612 −2.7574 domain 3 // 4q35 // 27295 /// NM_001114107 // NM_015886 // P115 // peptidaseinhibitor 15 // PI15 NM_015886 0.0312943 −2.78937 8q21.11 // 51050 /// ENST00000260 NM_003289 // TPM2 // tropomyosin 2 (beta) // TPM2 NM_003289 0.0272347 −2.80338 9p13 // 7169 /// NM_213674 // TPM2 NM_001458 // FLNC // filamin C, gamma // FLNC NM_001458 0.0113027 −2.80588 7q32-q35 // 2318 /// NM_001127487 // FL NM_006097 // MYL9 // myosin, light chain 9, MYL9 NM_006097 0.0412118 −2.81849 regulatory // 20q11.23 // 10398 /// NM_199460 // CACNA1C // calcium CACNA1C NM_199460 0.00694625 −2.83404 channel, voltage-dependent, L type, alpha 1C sub NM_001232 // CASQ2 // calsequestrin 2 CASQ2 NM_001232 0.0349505 −2.84886 (cardiac muscle) // 1p13.3-p11 // 845 /// NM_001193460 // MSRB3 // methionine MSRB3 NM_001193460 0.0108076 −2.84899 sulfoxide reductase B3 // 12q14.3 // 253827 NM_001456 // FLNA // filamin A, alpha // FLNA NM_001456 0.0164878 −2.86026 Xq28 // 2316 /// NM_001110556 // FLNA/ NM_006366 // CAP2 // CAP, adenylate CAP2 NM_006366 0.00596997 −2.89059 cyclase-associated protein, 2 (yeast) // 6p2 NM_001031701 // NT5DC3 // 5′- NT5DC3 NM_001031701 0.0464686 −2.90347 nucleotidase domain containing 3 // 12q22-q23.1 // NM_003999 // OSMR // oncostatin M OSMR NM_003999 0.0324297 −2.92605 receptor // 5p13.1 // 9180 /// NM_001168355 // NM_001885 // CRYAB // crystallin, alpha B // CRYAB NM_001885 0.0163674 −2.96044 11q22.3-q23.1 // 1410 /// ENST00000 NM_000517 // HBA2 // hemoglobin, alpha 2 // HBA2 NM_000517 0.0195505 −3.10109 16p13.3 // 3040 /// BC101846 // HBA1 NM_000558 // HBA1 // hemoglobin, alpha 1 // HBA1 NM_000558 0.0195505 −3.10109 16p13.3 // 3039 /// BC101846 // HBA1 NM_004282 // BAG2 // BCL2-associated BAG2 NM_004282 0.0108668 −3.11097 athanogene 2 // 6p12.1-p11.2 // 9532 /// EN NM_022135 // POPDC2 // popeye domain POPDC2 NM_022135 0.0219995 −3.1427 containing 2 // 3q13.33 // 64091 /// ENST00 NM_001001522 // TAGLN // transgelin // TAGLN NM_001001522 0.0148609 −3.35842 11q23.2 // 6876 /// NM_003186 // TAGLN // NM_212482 // FN1 // fibronectin 1 // 2q34 // FN1 NM_212482 0.00987492 −3.43741 2335 /// NM_002026 // FN1 // fibron NM_133477 // SYNPO2 // synaptopodin 2 // SYNPO2 NM_133477 0.0241716 −3.56252 4q26 // 171024 /// NM_001128933 // SYNP NM_000450 // SELE // selectin E // 1q22-q25 // SELE NM_000450 0.0460446 −3.56423 6401 /// ENST00000333360 // SELE NR_029686 // MIR145 // microRNA 145 // MIR145 NR_029686 0.0119026 −3.58867 5q32 // 406937 /// NR_027180 // LOC728264 NM_022648 // TNS1 // tensin 1 // 2q35-q36 // TNS1 NM_022648 0.00555851 −3.61273 7145 /// ENST00000171887 // TNS1 // NM_001615 // ACTG2 // actin, gamma 2, ACTG2 NM_001615 0.0379131 −3.62826 smooth muscle, enteric // 2p13.1 // 72 /// NM_022844 // MYH11 // myosin, heavy MYH11 NM_022844 0.0240032 −3.66415 chain 11, smooth muscle // 16p13.11 // 4629 NM_002205 // ITGA5 // integrin, alpha 5 ITGA5 NM_002205 0.0207749 −3.82521 (fibronectin receptor, alpha polypeptide NM_001299 // CNN1 // calponin 1, basic, CNN1 NM_001299 0.0413103 −3.84711 smooth muscle // 19p13.2-p13.1 // 1264/ NM_001034954 // SORBS1 // sorbin and SORBS1 NM_001034954 0.00399907 −3.89048 SH3 domain containing 1 // 10q23.33 // 1058 NM_001927 // DES // desmin // 2q35 // 1674 /// DES NM_001927 0.0268126 −3.90558 ENST00000373960 // DES // desmin NM_144617 // HSPB6 // heat shock protein, HSPB6 NM_144617 0.0145209 −3.90993 alpha-crystallin-related, B6 // 19q13. NM_015424 // CHRDL2 // chordin-like 2 // CHRDL2 NM_015424 0.0247555 −4.23746 11q14 // 25884 /// ENST00000263671 // C NM_000518 // HBB // hemoglobin, beta // HBB NM_000518 0.0255665 −4.3277 11p15.5 // 3043 /// ENST00000335295 // H NM_002160 // TNC // tenascin C // 9q33 // TNC NM_002160 0.0126641 −4.4403 3371 /// ENST00000350763 // TNC // ten NM_006198 // PCP4 // Purkinje cell protein PCP4 NM_006198 0.0340302 −4.51736 4 // 21q22.2 // 5121 /// ENST00000328

TABLE 3 LSMean LSMean p-value Ratio Fold-Change Gene (CC) (UC) (CC vs. UC) (CC vs. UC) (CC vs. UC) ALOX5AP 6.5368 7.2279 0.153036 0.61938 −1.61452 CD53 8.15458 8.56075 0.417119 0.754626 −1.32516 CLEC4D 3.24889 4.27055 0.168864 0.49255 −2.03025 CYP4F3LP 4.37787 5.62699 0.0584598 0.420703 −2.37697 DEFA5 12.7353 5.85087 0.00182525 118.145 118.145 IL6 4.49499 6.78934 0.167391 0.203859 −4.90534 RBP2 5.30406 2.51937 0.282548 6.8909 6.8909 SAA1 8.41257 9.68772 0.0988763 0.413184 −2.42023 SAA2 5.51497 5.96818 0.575901 0.730416 −1.36908 SCARNA8 11.4046 12.1182 0.132287 0.609768 −1.63997 SMAD4 8.62326 9.2041 0.00233383 0.668575 −1.49572 SNORD13 17.8866 18.7927 0.00409278 0.533634 −1.87394 SNORD13P 7.23404 7.74883 0.0839705 0.699895 −1.42879 SNORD28 15.5932 16.2543 0.00995582 0.632425 −1.58122 STAP1 5.59895 6.62415 0.211401 0.491342 −2.03524 UNQ2550 2.97077 3.95127 0.0386757 0.506805 −1.97314 

What is claimed is:
 1. A method of measuring DEFA5 protein in a patient suffering from or at risk of inflammatory bowel disease (IBD), said method comprising: obtaining a sample from the patient; and measuring at least one of an expression of DEFA5 and a concentration of DEFA5 in the sample using an anti-DEFA5 antibody.
 2. A method of treating a patient suffering from or at risk of inflammatory bowel disease (IBD), said method comprising: performing the method of measuring DEFA5 in the patient according to claim 1; and performing an intervention on the patient to treat Crohn's disease.
 3. The method of claim 1, comprising: comparing the expression of DEFA5 or the concentration of DEFA5 in the sample to a benchmark value that is typical of a subject not suffering from Crohn's disease; and diagnosing Crohn's disease if the expression of DEFA5 or the concentration of DEFA5 in the sample significantly exceeds the benchmark value.
 4. The method of claim 2, comprising: comparing the expression of DEFA5 or the concentration of DEFA5 in the sample to a benchmark value that is typical of a subject not suffering from Crohn's disease; and diagnosing Crohn's disease if the expression of DEFA5 or the concentration of DEFA5 in the sample significantly exceeds the benchmark value.
 5. The method of any one of claims 3-4, wherein the benchmark value is about 1 ng/mL DEFA5.
 6. The method of any one of claims 3-4, wherein the benchmark value is 1 ng/mL DEFA5.
 7. The method of any one of claims 1-4, wherein the expression of DEFA5 or the concentration of DEFA5 in the sample exceeds a benchmark value that is typical of a subject not suffering from Crohn's disease.
 8. The method of any one of claims 1-4, wherein the concentration of DEFA5 in the sample exceeds about 1 ng/mL.
 9. The method of any one of claims 1-4, wherein the sample is intestinal tissue, and comprising measuring the concentration of DEFA5 by: immunostaining the sample with an anti-DEFA5 immunostaining agent comprising the anti-DEFA5 antibody; and measuring the percentage of cells in the sample that stain positive; wherein the percentage of cells in the sample that stain positive is at least 20%.
 10. The method of any one of claims 2-4, wherein the intervention is not effective to treat ulcerative colitis.
 11. The method of any one of claims 2-4, wherein the intervention is administration of a drug, to the exclusion of a surgery.
 12. The method of any one of claims 2-4, wherein the intervention is administration of a drug selected from the group consisting of: a vitamin supplement, an anti-inflammatory, a corticosteroid, prednisolone, methyl-prednisolone, oral budesonide, a 5-aminosalicylate, an immunosuppressant, azathioprine, mercaptopurine, an anti-TNF-alpha antibody, infliximab, adalimumab, certolizumab pegol, methotrexate, an anti-α4-integrin antibody, natalizumab, vedolizumab, an anti-interleukin antibody, ustekinumab, an antibacterial antibiotic, ciprofloxacin, metronidazole, an anticholinergic agent, propantheline, dicyclomine, hyoscyamine, a bile acid sequestrant, cholestyramine, colestipol, and colesevalm.
 13. The method of any one of claims 2-4, wherein the intervention is administration of a drug selected from the group consisting of: vitamin B12, vitamin D, calcium, certolizumab pegol, methotrexate, and natalizumab.
 14. The method of any one of claims 2-4, wherein the intervention is enteral nutrition therapy.
 15. The method of any one of claims 2-4, wherein the intervention is placement of the subject on a low fat diet.
 16. A method of treating a patient suffering from or at risk of inflammatory bowel disease (IBD), said method comprising: performing the method of measuring DEFA5 in the patient according to claim 1; and performing an intervention on the patient to treat ulcerative colitis.
 17. The method of claim 16, comprising: comparing the expression of DEFA5 or the concentration of DEFA5 in the sample to a benchmark value that is typical of a subject not suffering from Crohn's disease; and diagnosing ulcerative colitis if the expression of DEFA5 or the concentration of DEFA5 in the sample does not significantly exceed the benchmark value.
 18. The method of claim 16, wherein the benchmark value is about 1 ng/mL.
 19. The method of claim 16, wherein the benchmark value is 1 ng/mL.
 20. The method of any one of claims 16-17, wherein the expression of DEFA5 or the concentration of DEFA5 in the sample is below a benchmark value that is typical of a subject suffering from Crohn's disease.
 21. The method of claim 20, wherein the benchmark value is about 1 ng/mL.
 22. The method of claim 20, wherein the benchmark value is 1 ng/mL.
 23. The method of any one of claims 16-17, wherein the expression or concentration of DEFA5 in the sample is measured to be significantly less than in a control sample from a subject suffering from Crohn's disease.
 24. The method of any one of claims 16-17, wherein the sample is intestinal tissue, and comprising measuring the concentration of DEFA5 by: immunostaining the sample with an anti-DEFA5 immunostaining agent comprising the anti-DEFA5 antibody; and measuring the percentage of cells in the sample that stain positive; wherein the percentage of cells in the sample that stain positive is less than 10%.
 25. The method of any one of claims 16-17, wherein the intervention is not effective to treat Crohn's disease.
 26. The method of any one of claims 16-17, wherein the intervention is a surgery selected from the group consisting of: a proctocolectomy, and an ileal pouch anal anastomosis.
 27. The method of any one of claims 16-17, wherein the intervention is administration of a drug selected from the group consisting of: an iron supplement, an anti-inflammatory, a corticosteroid, hydrocortisone, cortisone, prednisolone, a 5-aminosalicylate, an immunosuppressant, azathioprine, mercaptopurine, cyclosporine, an anti-TNF-alpha antibody, infliximab, adalimumab, golimumab, methotrexate, an anti-α4-integrin antibody, vedolizumab, an antibacterial antibiotic, ciprofloxacin, metronidazole, suppository mesalazine, enema mesalazine, olsalazine, balsalazide, enema budesonide, tacrolimus, and a combination of any of the foregoing.
 28. The method of any one of claims 16-17, wherein the intervention is administration of a drug selected from the group consisting of: cyclosporine, and golimumab.
 29. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody is selected from the group consisting of: Anti-alpha 5 Defensin antibody [EPR14309(B)] from ABCAM, Cambridge, United Kingdom; Anti-alpha 5 Defensin antibody (ab167591) from ABCAM, Cambridge, United Kingdom; Anti-alpha 5 Defensin antibody [8C8](Catalogue #ab90802) from ABCAM, Cambridge, United Kingdom; Defensin 5 Monoclonal Antibody (8C8) (Catalogue #MA1-46026) from THERMO FISHER SCIENTIFIC INC., Waltham, Mass.; Anti-Alpha Defensin-5 (DEFA5) Antibody, clone 8C8 (Catalogue #MABF31) from MILLIPORESIGMA, Burlington, Mass.; Defensin 5 Antibody LS-C50934 (Catalogue #LS-C50934-100) from LSBIO, Seattle, Wash.; Defensin alpha 5 Antibody (8C8) (Catalogue #NB110-60002/NB110-60002SS) from NOVUS BIOLOGICALS, Littleton, Colo.; Defensin alpha 5 Antibody (8C8) (Catalogue #NBP1-84282) from NOVUS BIOLOGICALS, Littleton, Colo.; Defensin alpha 5 antibody (Catalogue #orb156565) from BIORBYT, Cambridge, United Kingdom; Defensin alpha 5 Antibody (Catalogue #bs-4313R) from BIOSS INC., Woburn, Mass.; Defensin alpha 5 antibody [N1C3] (Catalogue #GTX116079) from GENETEX, INC., Irvine, Calif.; Anti-DEFA5 Antibody (HPA015775) from ATLAS ANTIBODIES, Bromma, Sweden; and α-defensin 5 antibody (catalogue #53997) from SANTA CRUZ BIOTECHNOLOGY, INC., Dallas, Tex.
 30. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody is α-defensin 5 antibody (catalogue #53997) from SANTA CRUZ BIOTECHNOLOGY, INC., Dallas, Tex.
 31. The method of any one of claims 1-4 and 12-13, wherein the anti-DEFA5 antibody is a kappa light chain polypeptide subunit.
 32. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody displays a higher affinity for DEFA5 than for one or more of the following proteins: DEFA1, DEFA2, DEFA3, DEFA4, and DEFA6.
 33. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody displays a higher affinity for DEFA5 than for DEFA1 and DEFA6.
 34. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody has a Kos (M) with one or both of DEFA1 and DEFA6 that is greater than one of the following values: 10⁻¹⁰, 10⁻⁹, 10⁻⁸, 10⁻⁷, 10⁻⁶, 10⁻⁵, 10⁻⁴, 10⁻³, 10⁻², and 10⁻¹.
 35. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody has a Kos (M) with DEFA5 that is less than one of the following values: 10⁻¹², 10⁻¹¹, 10⁻¹⁰, 10⁻⁹, 10⁻⁸, and 10⁻⁷.
 36. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody recognizes one or more of the P, B, and M binding sites on DEFA5.
 37. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody recognizes an epitope binding region having at least 90% sequence identity to positions 51-94 of SEQ ID NO:
 1. 38. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody recognizes an epitope binding region having 100% sequence identity to positions 51-94 of SEQ ID NO:
 1. 39. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody does not recognize an epitope binding region having at least 90% sequence identity to positions 1-49 of SEQ ID NO:
 1. 40. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody does not recognize an epitope binding region having 100% sequence identity to positions 1-49 of SEQ ID NO:
 1. 41. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody is a mammalian antibody.
 42. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody is an anti-human DEFA5 antibody.
 43. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody is used as part of an assay selected from the group consisting of: a radioimmunoassays, an immunohistochemistry assay, a competitive-binding assay, a Western Blot analysis, an ELISA assays, two-dimensional gel electrophoresis, an enzyme immunoassay, a sandwich immunoassays, a precipitin reaction, a gel diffusion reaction, an immunodiffusion assay, an agglutination assay, a complement-fixation assay, an immunoradiometric assay, a fluorescent immunoassay, a protein A immunoassays, and an immunoelectrophoresis assay.
 44. The method of any one of claims 1-4 and 16-17, wherein the anti-DEFA5 antibody is used as part of an enzyme-linked immunosorbent assay (ELISA).
 45. The method of any one of claims 1-4 and 16-17, wherein the sample is intestinal tissue.
 46. The method of any one of claims 1-4 and 16-17, wherein the sample is stool.
 47. The method of any one of claims 1-4 and 16-17, wherein the sample is blood.
 48. The method of any one of claims 1-4 and 16-17, wherein the sample is serum.
 49. The method of any one of claims 1-4 and 16-17, wherein the DEFA5 is human DEFA5.
 50. The method of any one of claims 1-4 and 16-17, wherein the expression of DEFA5 or the concentration of DEFA5 is measured in the sample ex vivo.
 51. The method of any one of claims 1-4 and 16-17, wherein the expression of DEFA5 or the concentration of DEFA5 is measured in the sample in vitro.
 52. The method of any one of claims 1-4 and 16-17, wherein the patient is suffering from IBD.
 53. The method of any one of claims 1-4 and 16-17, wherein the patient displays one or more of severe diarrhea, abdominal pain, fatigue, and weight loss.
 54. The method of any one of claims 1-4 and 16-17, wherein the patient displays severe diarrhea, abdominal pain, fatigue, and weight loss.
 55. A kit for measuring DEFA5 in a sample, the kit comprising: an assay comprising an anti-DEFA5 antibody; and a sample container configured to contain a sample selected from: a stool sample, a blood sample, a bowel tissue sample, and a serum sample.
 56. The kit of claim 55, wherein said kit is for the diagnosis of inflammatory bowel disease.
 57. The kit of claim 55, wherein the kit comprises a sampling tool selected from the group consisting of: a stool sample collector, a blood sample collector, a serum sample collector, and a bowel tissue collector.
 58. The kit of claim 55, comprising a sampling tool selected from a biopsy instrument, a rectal lavage kit, a swab, a blood sampler, and a vacutainer.
 59. A method of diagnosing and treating Crohn's disease in a subject suffering from inflammatory bowel disease, the method comprising: obtaining a sample from the patient; measuring the concentration of human DEFA5 in the sample using an anti-DEFA5 antibody having a higher affinity for human DEFA5 than for either of human DEFA1 or human DEFA6; comparing the concentration of human DEFA5 in the sample to a benchmark value that is typical of a subject not suffering from Crohn's disease; diagnosing Crohn's disease if the concentration of DEFA5 in the sample significantly exceeds the benchmark value; and treating the subject for Crohn's disease by way of a non-surgical intervention.
 60. The novel and non-obvious embodiments and features disclosed herein. 